Proteopedia - User contributions [en]

User:Andre Wu Le Chun/Sandbox 1

2020-08-01T01:32:21Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), which consists of the residues Arg319-Phe541, is responsible for binding to the host cell receptor, and the S2 subunit, which is responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure,

In the RBD, a β-sheet formed by 5 units of antiparallel β strands with units of α-helices and loops in between can be found. The receptor binding motif is located in a fragment that contains the β5 and β6 strands, α4 and α5 helices and loops.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block conformational changes of the protein and its biding and fusion mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that moment, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed. In order for the biding to happen 17 amino acid residues of the RBD interact with 20 amino acid residues of the receptor ACE2. It is important to consider the receptor binding domain similarity of both the SARS-CoV and the SARS-CoV-2. 14 amino acid positions are shared between the two conoraviruses RBD, these include Tyr449/Tyr436, Tyr453/Tyr440, Asn487/Asn473, Tyr489/Tyr475, Gly496/Gly482, Thr500/Thr486, Gly502/Gly488 and Tyr505/Tyr491, which are identical, and other 6 amino acid positions with altered residues. Also in the RBD, hydrophilic interctions such as 13 hydrogen bonds and 3 salt bridges can be found, tyrosine residues, which include Tyt449, Tyr489 and Tyr505, form hydrogen-bond interactions with polar hydroxil groups and in the complex formed by the spike protein and ACE2, a chain of Asn90-linked NAG-NAG-β-d-mannose, that may be useful for the bindin process can be found.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-08-01T01:29:39Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), which consists of the residues Arg319-Phe541, is responsible for binding to the host cell receptor, and the S2 subunit, which is responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure,

In the RBD, a β-sheet formed by 5 units of antiparallel β strands with units of α-helices and loops in between can be found. The receptor binding motif is located in a fragment that contains the β5 and β6 strands, α4 and α5 helices and loops. Also in the RBD, 9 cysteine residues can be found. Disulfide bonds are formed by four pairs of the cysteine residues previously mentioned and from those, 3 help to stabilize the β-sheet in the core, while the remaining pair has the role of connecting the loops in the farthest end of the receptor binding motif.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block conformational changes of the protein and its biding and fusion mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that moment, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed. In order for the biding to happen 17 amino acid residues of the RBD interact with 20 amino acid residues of the receptor ACE2. It is important to consider the receptor binding domain similarity of both the SARS-CoV and the SARS-CoV-2. 14 amino acid positions are shared between the two conoraviruses RBD, these include Tyr449/Tyr436, Tyr453/Tyr440, Asn487/Asn473, Tyr489/Tyr475, Gly496/Gly482, Thr500/Thr486, Gly502/Gly488 and Tyr505/Tyr491, which are identical, and other 6 amino acid positions with altered residues. Also in the RBD, hydrophilic interctions such as 13 hydrogen bonds and 3 salt bridges can be found, tyrosine residues, which include Tyt449, Tyr489 and Tyr505, form hydrogen-bond interactions with polar hydroxil groups and in the complex formed by the spike protein and ACE2, a chain of Asn90-linked NAG-NAG-β-d-mannose, that may be useful for the bindin process can be found.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-07-31T21:33:08Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), which consists of the residues Arg319-Phe541, is responsible for binding to the host cell receptor, and the S2 subunit, which is responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure,

In the RBD, a β-sheet formed by 5 units of antiparallel β strands with units of α-helices and loops in between can be found. The receptor binding motif is located in a fragment that contains the β5 and β6 strands, α4 and α5 helices and loops. Also in the RBD, 9 cysteine residues can be found. Disulfide bonds are formed by four pairs of the cysteine residues previously mentioned and from those, 3 help to stabilize the β-sheet in the core, while the remaining pair has the role of connecting the loops in the farthest end of the receptor binding motif.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block conformational changes of the protein and its biding and fusion mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that moment, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed. In order for the biding to happen 17 amino acid residues of the RBD interact with 20 amino acid residues of the receptor ACE2. It is important to consider the receptor binding domain similarity of both the SARS-CoV and the SARS-CoV-2. 14 amino acid positions are shared between the two conoraviruses RBD, these include Tyr449/Tyr436, Tyr453/Tyr440, Asn487/Asn473, Tyr489/Tyr475, Gly496/Gly482, Thr500/Thr486, Gly502/Gly488 and Tyr505/Tyr491, which are identical, and other 6 amino acid positions with altered residues. Also in the RBD, hydrophilic interctions such as 13 hydrogen bonds and 3 salt bridges can be found, tyrosine residues, which include Tyt449, Tyr489 and Tyr505, form hydrogen-bond interactions with polar hydroxil groups and in the complex formed by the spike protein and ACE2, a chain of Asn90-linked NAG-NAG-β-d-mannose, that may be useful for the bindin process can be found.
[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-07-31T20:44:06Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), which consists of the residues Arg319-Phe541, is responsible for binding to the host cell receptor, and the S2 subunit, which is responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure,

In the RBD, a β-sheet formed by 5 units of antiparallel β strands with units of α-helices and loops in between can be found. The receptor binding motif is located in a fragment that contains the β5 and β6 strands, α4 and α5 helices and loops. Also in the RBD, 9 cysteine residues can be found. Disulfide bonds are formed by four pairs of the cysteine residues previously mentioned and from those, 3 help to stabilize the β-sheet in the core, while the remaining pair has the role of connecting the loops in the farthest end of the receptor binding motif.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block conformational changes of the protein and its biding and fusion mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that moment, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed. In order for the biding to happen 17 amino acid residues of the RBD interact with 20 amino acid residues of the receptor ACE2. It is important to consider the receptor binding domain similarity of both the SARS-CoV and the SARS-CoV-2. 14 amino acid positions are shared between the two conoraviruses RBD, these include Tyr449/Tyr436, Tyr453/Tyr440, Asn487/Asn473, Tyr489/Tyr475, Gly496/Gly482, Thr500/Thr486, Gly502/Gly488 and Tyr505/Tyr491, which are identical, and other 6 amino acid positions with altered residues. Also in the RBD hydrophilic interctions such as 13 hydrogen bonds and 3 salt bridges can be found

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-07-31T07:48:54Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, which is responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure,

In the RBD, a β-sheet formed by 5 units of antiparallel β strands with units of α-helices and loops in between can be found. The receptor binding motif is located in a fragment that contains the β5 and β6 strands, α4 and α5 helices and loops. Also in the RBD, 9 cysteine residues can be found. Disulfide bonds are formed by four pairs of the cysteine residues previously mentioned and from those, 3 help to stabilize the β-sheet in the core, while the remaining pair has the role of connecting the loops in the farthest end of the receptor binding motif.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block conformational changes of the protein and its biding and fusion mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that moment, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed. In order for the biding to happen 17 amino acid residues of the RBD interact with 20 amino acid residues of the receptor ACE2. Similarly to the SARS-CoV's RBD, the

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-07-31T03:08:49Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, which is responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure,

In the RBD, a β-sheet formed by 5 units of antiparallel β strands with units of α-helices and loops in between can be found. The receptor binding motif is located in a fragment that contains the β5 and β6 strands, α4 and α5 helices and loops. Also in the RBD, 9 cysteine residues can be found. Disulfide bonds are formed by four pairs of the cysteine residues previously mentioned and from those, 3 help to stabilize the β-sheet in the core, while the remaining pair has the role of connecting the loops in the farthest end of the receptor binding motif.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block conformational changes of the protein and its biding and fusion mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that moment, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-07-28T19:34:21Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, which is responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure, in ithe RBD, a β-sheet formed by 5 units of β strands with units of α-helices and loops in between can be found.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block conformational changes of the protein and its biding and fusion mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that moment, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-06-22T13:49:41Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, which is responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure, units of beta-sheets, alpha-helices and loops can be observed thoughout the protein.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block conformational changes of the protein and its biding and fusion mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that moment, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-06-22T13:20:26Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, which is responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure, units of beta-sheets, alpha-helices and loops can be observed thoughout the protein.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block conformational changes of the protein and its biding and fusion mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that instance, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-06-22T02:01:07Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, which is responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure, units of beta-sheets, alpha-helices and loops can be observed thoughout the protein.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block conformational changes of the protein and its biding and fusion mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that instance, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T22:04:45Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure, units of beta-sheets, alpha-helices and loops can be observed thoughout the protein.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that instance, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian &

Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.

Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

Walls, Alexandra & Park, Young-Jun & Tortorici, M. & Wall, Abigail & Mcguire, Andrew & Veesler, David. (2020). Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. 10.1101/2020.02.19.956581.

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T22:02:03Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure, units of beta-sheets, alpha-helices and loops can be observed thoughout the protein.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that instance, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>

<references/>
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian & Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.
Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T22:01:38Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure, units of beta-sheets, alpha-helices and loops can be observed thoughout the protein.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that instance, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>
== References ==
Hoffmann, Markus & Kleine-Weber, Hannah & Schroeder, Simon & Krüger, Nadine & Herrler, Tanja & Erichsen, Sandra & Schiergens, Tobias & Herrler, Georg & Wu, Nai-Huei & Nitsche, Andreas & Müller, Marcel & Drosten, Christian & Pöhlmann, Stefan. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 181. 10.1016/j.cell.2020.02.052.
Tortorici, M. Alejandra & Veesler, David. (2019). Structural insights into coronavirus entry. 10.1016/bs.aivir.2019.08.002.

<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T21:48:10Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regarding its secundary structure, units of beta-sheets, alpha-helices and loops can be observed thoughout the protein.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that instance, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
https://www.sciencedirect.com/science/article/pii/S0092867420302294
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T21:44:18Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regardind its secundary structure, units of beta-sheets, alpha-helices and loops can be observed thoughout the protein.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that instance, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
https://www.sciencedirect.com/science/article/pii/S0092867420302294
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T21:41:19Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, a v shaped subunit which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regardind its secundary structure, units of beta-sheets, alpha-helices and loops can be observed thoughout the protein.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms is the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore, resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of the receptor. At that instance, the spike protein is found in a "up" conformation. Due to the existence of four amino acids in between the 680 and 685 positions, a furin cleavage site is featured in the protein. Once this site is cleaved by host's furins, a later cleavage at S2' by a serine protease, TMPRSS2, happens in order to allow the activation of the fusion mechanism. Lastly, the spike protein makes a high affinity bond with ACE2 at the order of 15nM and a complex of spike protein and ACE2, as shown in figure 3, is formed.

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).
[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (Goodsell, D., 2020)
</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
https://www.sciencedirect.com/science/article/pii/S0092867420302294
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T20:56:26Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that make the binding domain assume a up conformation, thus, exposing the spike protein to its target receptor.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. Regardind its secundary structure, units of beta-sheets, alpha-helices and loops can be observed thoughout the protein.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
As the name implies, The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing COVID-19. These include the development of vaccines based on antibodies that are able to block protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of target cell. Due to the existence of four amino acids in between the S1 and S2, a furin cleavage site is featured in the protein. The cleavage of this site has potential relevance as it could lead to later priming at the S2' site by a serine protease, TMPRSS2. Once attached on the surface of ACE2, the cleavage of S2' happens and the fusion mechanism is activated. Then, the protein goes through conformational changes, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name. It binds itself to the ACE2 with high affinity (15nM). In order to activate infection, the spike protein is cleaved by TMPRSS2, a host's serine protease, also fundamental for the viral infection. Furine cleavage site

[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).
[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (
</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
https://www.sciencedirect.com/science/article/pii/S0092867420302294
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T20:08:04Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

<scene name='84/844931/6vsb/2'>6vsb</scene> is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, which contains the receptor binding domain (<scene name='84/844931/S_receptor-binding_domain/1'>RBD</scene>), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that start from a pre-fusion conformation to a stable post-fusion conformation, in which the receptor-binding domain assumes a up conformation.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. In the Receptor binding domain, units of beta-sheets, alpha-helices and loops can be observed.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
As the name implies, The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of target cell. Due to the existence of four amino acids in between the S1 and S2, a furin cleavage site is featured in the protein. The cleavage of this site has potential relevance as it could lead to later priming at the S2' site by a serine protease, TMPRSS2. Once attached on the surface of ACE2, the cleavage of S2' happens and the fusion mechanism is activated. Then, the protein goes through conformational changes, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name. It binds itself to the ACE2 with high affinity (15nM). In order to activate infection, the spike protein is cleaved by TMPRSS2, a host's serine protease, also fundamental for the viral infection. Furine cleavage site
[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).
[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (
</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
https://www.sciencedirect.com/science/article/pii/S0092867420302294
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T20:05:41Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, which contains the receptor binding domain (RBD), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that start from a pre-fusion conformation to a stable post-fusion conformation, in which the receptor-binding domain assumes a up conformation.

<scene name='84/844931/S_receptor-binding_domain/1'>Text To Be Displayed</scene>

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. In the Receptor binding domain, units of beta-sheets, alpha-helices and loops can be observed.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
As the name implies, The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of target cell. Due to the existence of four amino acids in between the S1 and S2, a furin cleavage site is featured in the protein. The cleavage of this site has potential relevance as it could lead to later priming at the S2' site by a serine protease, TMPRSS2. Once attached on the surface of ACE2, the cleavage of S2' happens and the fusion mechanism is activated. Then, the protein goes through conformational changes, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name. It binds itself to the ACE2 with high affinity (15nM). In order to activate infection, the spike protein is cleaved by TMPRSS2, a host's serine protease, also fundamental for the viral infection. Furine cleavage site
[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).
[[Image:SpikeACE2.jpg|340px|]]
Figure 3: Spike protein and ACE2 bound together (
</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
https://www.sciencedirect.com/science/article/pii/S0092867420302294
<references/>

File:SpikeACE2.jpg

2020-06-21T19:54:32Z

Andre Wu Le Chun:

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T19:31:29Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, which contains the receptor binding domain (RBD), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that start from a pre-fusion conformation to a stable post-fusion conformation, in which the receptor-binding domain assumes a up conformation.

<scene name='84/844931/S_receptor-binding_domain/1'>Text To Be Displayed</scene>

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown in the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. In the Receptor binding domain, units of beta-sheets, alpha-helices and loops can be observed.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
As the name implies, The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of target cell. Due to the existence of four amino acids in between the S1 and S2, a furin cleavage site is featured in the protein. The cleavage of this site has potential relevance as it could lead to later priming at the S2' site by a serine protease, TMPRSS2. Once attached on the surface of ACE2, the cleavage of S2' happens and the fusion mechanism is activated. Then, the protein goes through conformational changes, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name. It binds itself to the ACE2 with high affinity (15nM). In order to activate infection, the spike protein is cleaved by TMPRSS2, a host's serine protease, also fundamental for the viral infection. Furine cleavage site
[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
https://www.sciencedirect.com/science/article/pii/S0092867420302294
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T18:50:54Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, which contains the receptor binding domain (RBD), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that start from a pre-fusion conformation to a stable post-fusion conformation, in which the receptor-binding domain assumes a up conformation.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however, as shown at the figure bellow, it has inserted amino acids that indicate a furin like cleavage site in the S1/S2 boundary. that must be primed in order to enable the viral pathogenicity. In the Receptor binding domain, units of beta-sheets, alpha-helices and loops can be observed.

[[Image:Spike amino acids.jpg|500px|]]
Figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
As the name implies, The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of target cell. Due to the existence of four amino acids in between the S1 and S2, a furin cleavage site is featured in the protein. The cleavage of this site has potential relevance as it could lead to later priming at the S2' site by a serine protease, TMPRSS2. Once attached on the surface of ACE2, the cleavage of S2' happens and the fusion mechanism is activated. Then, the protein goes through conformational changes, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name. It binds itself to the ACE2 with high affinity (15nM). In order to activate infection, the spike protein is cleaved by TMPRSS2, a host's serine protease, also fundamental for the viral infection. Furine cleavage site
[[Image:Spike.jpg|500px|]]
Figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T18:43:26Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, which contains the receptor binding domain (RBD), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that start from a pre-fusion conformation to a stable post-fusion conformation, in which the receptor-binding domain assumes a up conformation.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however it has inserted amino acid that indicate a furin like cleavage site in the S1/S2 boundary, that must be primed in order to enable the viral pathogenicity. In the Receptor binding domain, units of beta-sheets, alpha-helices and loops can be observed.

[[Image:Spike amino acids.jpg|500px|]]
figure 1: Alignment of S in between multiple SARS-CoV (Walls et al., 2020)

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
As the name implies, The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of target cell. Due to the existence of four amino acids in between the S1 and S2, a furin cleavage site is featured in the protein. The cleavage of this site has potential relevance as it could lead to later priming at the S2' site by a serine protease, TMPRSS2. Once attached on the surface of ACE2, the cleavage of S2' happens and the fusion mechanism is activated. Then, the protein goes through conformational changes, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name. It binds itself to the ACE2 with high affinity (15nM). In order to activate infection, the spike protein is cleaved by TMPRSS2, a host's serine protease, also fundamental for the viral infection. Furine cleavage site
[[Image:Spike.jpg|500px|]]
figure 2: Alignment between S protein of SARS and SARS-2 (Hoffmann et al., 2020).

</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
<references/>

File:Spike amino acids.jpg

2020-06-21T17:39:43Z

Andre Wu Le Chun:

File:Spike.jpg

2020-06-21T17:30:21Z

Andre Wu Le Chun: uploaded a new version of "Image:Spike.jpg"

File:Spike.jpg

2020-06-21T17:22:03Z

Andre Wu Le Chun:

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T07:02:34Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='340' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. It is composed by two subunits that are fundamental for the virus entry in the cell: The S1 subunit, which contains the receptor binding domain (RBD), is responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. In order to allow the binding of the RBD in S1 with the host cell, the spike protein goes through conformational changes that start from a pre-fusion conformation to a stable post-fusion conformation, in which the receptor-binding domain assumes a up conformation.

This protein also shares amino acid sequence identity of 76% with SARS-CoV, however it has inserted amino acid that indicate a furin like cleavage site in the S1/S2 boundary, that must be primed in order to enable the viral pathogenicity. In the Receptor binding domain, units of beta-sheets, alpha-helices and loops can be observed.

== Function ==
The spike glycoprotein binds the viral structure to the hosts cell's angiotensin-converting enzime 2 ([[1r42]]). Once bound, it starts the fusion of viral and cellular membrane, therefore enabling the pathogenicity and spread of the virus.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale coronavirus epidemics in 2020.
As the name implies, The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domain of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that receptor-binding domain becomes available to connect itself to the peptidase domain of target cell. Due to the existence of four amino acids in between the S1 and S2, a furin cleavage site is featured in the protein. The cleavage of this site has potential relevance as it could lead to later priming at the S2' site by a serine protease, TMPRSS2. Once attached on the surface of ACE2, the cleavage of S2' happens and the fusion mechanism is activated. Then, the protein goes through conformational changes, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name. It binds itself to the ACE2 with high affinity (15nM). In order to activate infection, the spike protein is cleaved by TMPRSS2, a host's serine protease, also fundamental for the viral infection. Furine cleavage site

</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-21T06:31:24Z

Andre Wu Le Chun:

User:Andre Wu Le Chun/Sandbox 1

2020-06-20T20:07:06Z

Andre Wu Le Chun:

User:Andre Wu Le Chun/Sandbox 1

2020-06-20T01:46:28Z

Andre Wu Le Chun:

User:Andre Wu Le Chun/Sandbox 1

2020-06-19T22:07:33Z

Andre Wu Le Chun:

File:6vsb.pse

2020-06-19T03:29:08Z

Andre Wu Le Chun: uploaded a new version of "Image:6vsb.pse"

File:6vsb.pse

2020-06-19T03:27:16Z

Andre Wu Le Chun: uploaded a new version of "Image:6vsb.pse"

User:Andre Wu Le Chun/Sandbox 1

2020-06-19T03:10:05Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='500' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. There are two subunits which are fundamental for the virus entry in the cell: the S1 subunit, responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes. It also assumes different conformations throughout the infection process: the pre-fusion conformation, the

== Function ==
The spike glycoprotein recognizes the hosts cell's angiotensin-converting enzime 2 [[http://proteopedia.org/wiki/index.php/1r42]] and binds itself on it, allowing the fusion of viral and cellular membrane, therefore enabling the viral infection.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domains of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, which is a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that determinants for the virus-cell binding. Due to the conformational movements, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name.

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
<references/>

File:6vsb.pse

2020-06-18T19:21:48Z

Andre Wu Le Chun:

User:Andre Wu Le Chun/Sandbox 1

2020-06-17T17:34:26Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='500' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. There are two subunits which are fundamental for the virus entry in the cell: the S1 subunit, responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes.

== Function ==
The spike glycoprotein recognizes the hosts cell's angiotensin-converting enzime 2 (ACE2) and binds itself on it, allowing the fusion of viral and cellular membrane, therefore enabling the viral infection.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domains of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2, which is a dimeric protein. Then, the S1 subunit moves, modifying the protein's conformation in way that determinants for the virus-cell binding. Due to the conformational movements, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name.

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-17T00:22:26Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='500' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. There are two subunits which are fundamental for the virus entry in the cell: the S1 subunit, responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes.

== Function ==
The spike glycoprotein recognizes the hosts cell's angiotensin-converting enzime 2 (ACE2) and binds itself on it, allowing the fusion of viral and cellular membrane, therefore enabling the viral infection.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domains of the protein, by the host's proteases could be a way of viral inhibition. Comprehending how the protein can be bound to antibodies could also help the scientific community to prepare for future SARS coronavirus outbreaks that may happen in the future

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2 receptor. Then, the S1 subunit moves, modifying the protein's conformation in way that determinants for the virus-cell binding. Due to the conformational movements, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name.

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-15T04:26:46Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='500' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. There are two subunits which are fundamental for the virus entry in the cell: the S1 subunit, responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes.

== Function ==
The spike glycoprotein recognizes the hosts cell's angiotensin-converting enzime 2 (ACE2) and binds itself on it, allowing the fusion of viral and cellular membrane, therefore enabling the viral infection.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Due to its role in the infection process, the spike glyprotein may be a potential target of studies that seek methods of preventing the COVID-19 disease. These include the development of vaccines based on the protein's structure of the protein and on it's recognition/biding mechanisms. For instance, avoiding the cleavage of the furin, located on the B domains of the protein, by the host's proteases could be a way of viral inhibition.

== Interaction with angiotensin-converting enzime 2 ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2 receptor. Then, the S1 subunit moves, modifying the protein's conformation in way that determinants for the virus-cell binding. Due to the conformational movements, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name.

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-14T18:24:52Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='500' side='right' caption='2019-nCoV spike glycoprotein with a single receptor-binding domain up. [[6vsb]]' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Structural highlights ==

6svb is a homotrimer transmembrane glycoprotein(S) protruding from the viral surface¹. There are two subunits which are fundamental for the virus entry in the cell: the S1 subunit, responsible for binding to the host cell receptor, and the S2 subunit, responsible for fusion of the viral and cellular membranes.

== Function ==
The spike glycoprotein reconizes the hosts cell's angiotensin-converting enzime 2 (ACE2) receptor and binds itself on it, allowing the fusion of viral and cellular membrane, therefore enabling the viral infection.

== Disease ==
6vsb is probably the protein that enabled the Sars-Cov-2 to enter human cells, rusulting therefore on the large scale epidemics in 2020.
The main symptoms of the COVID-19 were similar to the ones of common cold: fever, cough and tiredness, but with some stronger than the common cold: Chest pain, lost of smell and taste sense.
The main reason for the worst symptoms are the death of several types of cells in the lungs, causing severe loss of oxygenation, therefore resulting of gradual colapse of the respiratory system of the infected.

== Relevance ==
Potential target for antibodies. Development of vaccines based on the structure of the protein and on it's recognition/biding mechanisms.

== Interaction with angiotensin-converting enzime 2 receptor ==
The interaction between the 2019-nCov and the host cell begins with the recognition of the ACE2 receptor. Then, the S1 subunit moves, modifying the protein's conformation in way that determinants for the virus-cell binding. Due to the conformational movements, the protein structure assumes a conformation which is suitable for binding with the ACE2 receptor. At that instance, the spike protein is found in a "up" conformation, hence the protein's name.

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
¹https://www.sciencedirect.com/science/article/pii/S0065352719300284
²https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1.full
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-06-14T18:09:16Z

Andre Wu Le Chun:

User:Andre Wu Le Chun/Sandbox 1

2020-05-18T14:44:04Z

Andre Wu Le Chun:

User:Andre Wu Le Chun/Sandbox 1

2020-05-18T12:19:15Z

Andre Wu Le Chun:

User:Andre Wu Le Chun/Sandbox 1

2020-05-18T11:33:03Z

Andre Wu Le Chun:

User:Andre Wu Le Chun/Sandbox 1

2020-05-11T18:55:39Z

Andre Wu Le Chun:

==6vsb==
==Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up==
<StructureSection load='6vsb' size='500' side='right' caption='Sars-Cov-2 6vsb' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Andre Wu Le Chun/Sandbox 1

2020-05-11T17:57:52Z

Andre Wu Le Chun: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='6vsb' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='6vsb' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Andre Wu Le Chun/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Andre Wu Le Chun

2020-05-11T14:05:08Z

Andre Wu Le Chun:

* Full Real Name: Andre Wu Le Chun

* Position: Undergraduate

* Institution (NO ABBREVIATIONS): University of Sao Paulo.

* City, State/Province, Country: Sao Paulo - SP, Brazil

* Field of Expertise or Study: Undergraduate in protein class on Biosciences Institute – University of
Sao Paulo – Brazil

*[[User:Andre Wu Le Chun/Sandbox 1]]