Proteopedia - User contributions [en]

SARS-CoV-2 protein ORF7a

2020-10-26T21:39:23Z

Sabrina Staeb:

<SX viewer='molstar' load='6w37' size='350' side='right' caption='Accessory Protein 7a from SARS-CoV2 (PDB entry [[6w37]])' scene=''>

The genome of SARS-CoV-2 codes for an ORF1a/ ORF1ab (open reading frame) polyprotein containing sixteen non-structural proteins (NSP) and four structural proteins. Additionally, the genome comprises a variable number of open reading frames coding for accessory proteins. These accessory proteins (3a,b; 6; 7a,b; 8; 9b,c; 10) are not necessary for virus replication but might play a key role in pathogenesis <ref> Michel, Christian Jean; Mayer, Claudine; Poch, Olivier; Thompson, Julie Dawn (2020): Characterization of accessory genes in coronavirus genomes. In: Virol J 17 (1), S. 131. DOI: 10.1186/s12985-020-01402-1 </ref>.

== Overall Structure ==

The SARS-CoV-2 accessory protein 7a has high sequence similarity with one in SARS-CoV. In SARS-CoV, sequence analysis predicts that ORF7a codes for a type I transmembrane protein with 122 amino acids including a signal peptide at the N-terminus and a retrieval signal at the C-terminus <ref> Fielding, Burtram C.; Tan, Yee-Joo; Shuo, Shen; Tan, Timothy H. P.; Ooi, Eng-Eong; Lim, Seng Gee et al. (2004): Characterization of a unique group-specific protein (U122) of the severe acute respiratory syndrome coronavirus. In: Journal of Virology 78 (14), S. 7311–7318. DOI: 10.1128/JVI.78.14.7311-7318.2004.</ref>. The N-terminal ectodomain of ORF7a (SARS-CoV) consists of seven β-strands, compactly arranged in an [[immunoglobulin]]-like β-sandwich fold. These seven β-strands are arranged in two β-sheets containing four β-strands (A; G; F; C) in the first sheet and three (B; E; D) in the second one. Both sheets are amphipathic and with the hydrophobic side inwards closely packed against each other. The top of the ectodomain is defined by the BC, DE and FG loops and the bottom by the AB, CD and EF loops. The β-sandwich structure is stabilized by two disulphide bonds linking the sheets at opposite edges. At the bottom of the structure, a disulphide bridge connects a Cys8 of strand A with Cys43 at the end of strand E. At the top, Cys20 of the BC loop is linked to Cys54 at the end of strand F. Additional on top of the BED sheet , the DE loop protrudes from the structure and forms a groove together with the β-strands C and D. In the centre is a Glu18 which contributes to a negatively charged bottom of the mainly hydrophobic groove. This groove may be a potential site for ligand interaction due to its central negative electrostatic potential <ref> Hänel, Karen; Stangler, Thomas; Stoldt, Matthias; Willbold, Dieter (2006): Solution structure of the X4 protein coded by the SARS related coronavirus reveals an immunoglobulin like fold and suggests a binding activity to integrin I domains. In: Journal of biomedical science 13 (3), S. 281–293. DOI: 10.1007/s11373-005-9043-9 </ref>.

== Fuction ==

In cell culture, the polypeptide 7a of SARS-CoV with 85% sequence identity and 95.2% sequence similarity to SARS-CoV-2, seems to have diverse biological functions <ref> Vasilenko, Natalia; Moshynskyy, Igor; Zakhartchouk, Alexander (2010): SARS coronavirus protein 7a interacts with human Ap4A-hydrolase. In: Virol J 7, S. 31. DOI: 10.1186/1743-422X-7-31.</ref> <ref> Francis K. Yoshimoto (2020): The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19. In: Protein J 39 (3), S. 198–216. DOI: 10.1007/s10930-020-09901-4.</ref>. SARS-CoV 7a is predicted to induce apoptosis in human kidney epithelial cells by interaction with Bcl-XL. Bcl-XL belongs to a group of pro-survival proteins, the BCL-2 family, which prevent apoptosis in epithelial cells. The Interaction between SARS-7a and the C-terminal transmembrane domain of Bcl-XL may interfere with this pro-survival function, leading to apoptosis via the caspase-dependant pathway <ref> Tan, Yee-Joo; Fielding, Burtram C.; Goh, Phuay-Yee; Shen, Shuo; Tan, Timothy H. P.; Lim, Seng Gee; Hong, Wanjin (2004): Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway. In: Journal of Virology 78 (24), S. 14043–14047. DOI: 10.1128/JVI.78.24.14043-14047.2004. </ref> <ref> Tan, Ying-Xim; Tan, Timothy H. P.; Lee, Marvin J-R; Tham, Puay-Yoke; Gunalan, Vithiagaran; Druce, Julian et al. (2007): Induction of apoptosis by the severe acute respiratory syndrome coronavirus 7a protein is dependent on its interaction with the Bcl-XL protein. In: Journal of Virology 81 (12), S. 6346–6355. DOI: 10.1128/JVI.00090-07. </ref>. Additionally, interaction of SARS 7a with Ap4A, a hydrolase involved in processes such as cell proliferation, DNA-replication, apoptosis and RNA-processing, leads to downregulation of its hydrolase-activity followed by an increased production of AP4A, which may also contributes to the induction of apoptosis <ref> Vasilenko, Natalia; Moshynskyy, Igor; Zakhartchouk, Alexander (2010): SARS coronavirus protein 7a interacts with human Ap4A-hydrolase. In: Virol J 7, S. 31. DOI: 10.1186/1743-422X-7-31. </ref>. It is also possible that 7a plays a key role in cell cycle control. In HEK 293 cell, an overexpression of 7a led to inhibition of cell growth and induction of the G0/G1 phase cell cycle arrest. This arrest may favour coronavirus replication and exacerbate virus-induced pathogenicity <ref> Yuan, Xiaoling; Wu, Jie; Shan, Yajun; Yao, Zhenyu; Dong, Bo; Chen, Bo et al. (2006): SARS coronavirus 7a protein blocks cell cycle progression at G0/G1 phase via the cyclin D3/pRb pathway. In: Virology 346 (1), S. 74–85. DOI: 10.1016/j.virol.2005.10.015.
</ref>.

== See also ==
[[Coronavirus_Disease 2019 (COVID-19)]]
__NOTOC__
</SX>
== References ==
<references/>

SARS-CoV-2 protein ORF7a

2020-10-26T21:23:20Z

Sabrina Staeb:

<SX viewer='molstar' load='6w37' size='350' side='right' caption='Accessory Protein 7a from SARS-CoV2 (PDB entry [[6w37]])' scene=''>

The genome of SARS-CoV-2 codes for an ORF1a/ ORF1ab (open reading frame) polyprotein containing sixteen non-structural proteins (NSP) and four structural proteins. Additionally, the genome comprises a variable number of open reading frames coding for accessory proteins. These accessory proteins (3a,b; 6; 7a,b; 8; 9b,c; 10) are not necessary for virus replication but might play a key role in pathogenesis <ref> Michel, Christian Jean; Mayer, Claudine; Poch, Olivier; Thompson, Julie Dawn (2020): Characterization of accessory genes in coronavirus genomes. In: Virol J 17 (1), S. 131. DOI: 10.1186/s12985-020-01402-1 </ref>

== Overall Structure ==

The SARS-CoV-2 accessory protein 7a has high sequence similarity with one in SARS-CoV. In SARS-CoV, sequence analysis predicts that ORF7a codes for a type I transmembrane protein with 122 amino acids including a signal peptide at the N terminus and a retrieval signal at the C-terminus. <ref> Fielding, Burtram C.; Tan, Yee-Joo; Shuo, Shen; Tan, Timothy H. P.; Ooi, Eng-Eong; Lim, Seng Gee et al. (2004): Characterization of a unique group-specific protein (U122) of the severe acute respiratory syndrome coronavirus. In: Journal of Virology 78 (14), S. 7311–7318. DOI: 10.1128/JVI.78.14.7311-7318.2004.</ref> The N-terminal ectodomain of ORF7a (SARS-CoV) consists of seven β-strands, compactly arranged in an Immuno-globulin-like β-sandwich fold. These seven β-strands are arranged in two β-sheets containing four β-strands (A; G; F; C) in the first sheet and three (B; E; D) in the second one. Both sheets are amphipathic and with the hydrophobic side inwards closely packed against each other. The top of the ectodomain is defined by the BC, DE and FG loops and the bottom by the AB, CD and EF loops. The β-sandwich structure is stabilized by two disulphide bonds linking the sheets at opposite edges. At the bottom of the structure, a disulphide bridge connects a Cys8 of strand A with Cys43 at the end of strand E. At the top, Cys20 of the BC loop is linked to Cys54 at the end of strand F. Additional on top of the BED sheet , the DE loop protrudes from the structure and forms a groove together with the β-strands C and D. In the centre is a Glu18 which contributes to a negatively charged bottom of the mainly hydrophobic groove. This grove may be a potential site for ligand interaction due to its central negative electrostatic potential. <ref> Hänel, Karen; Stangler, Thomas; Stoldt, Matthias; Willbold, Dieter (2006): Solution structure of the X4 protein coded by the SARS related coronavirus reveals an immunoglobulin like fold and suggests a binding activity to integrin I domains. In: Journal of biomedical science 13 (3), S. 281–293. DOI: 10.1007/s11373-005-9043-9 </ref>.

== Fuction ==

In cell culture, the polypeptide 7a of SARS-CoV with 85% sequence identity and 95.2% sequence similarity to SARS-CoV-2, seems to have diverse biological functions. <ref> Vasilenko, Natalia; Moshynskyy, Igor; Zakhartchouk, Alexander (2010): SARS coronavirus protein 7a interacts with human Ap4A-hydrolase. In: Virol J 7, S. 31. DOI: 10.1186/1743-422X-7-31.</ref> <ref> Francis K. Yoshimoto (2020): The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19. In: Protein J 39 (3), S. 198–216. DOI: 10.1007/s10930-020-09901-4.</ref> SARS-CoV 7a is predicted to induce apoptosis in human kidney epithelial cells by interaction with Bcl-XL. Bcl-XL belongs to a group of pro-survival proteins, the BCL-2 family, which prevent apoptosis in epithelial cells. The Interaction between SARS-7a and the C-terminal transmembrane domain of Bcl-XL may interfere with this pro-survival function, leading to apoptosis via the caspase-dependant pathway. <ref> Tan, Yee-Joo; Fielding, Burtram C.; Goh, Phuay-Yee; Shen, Shuo; Tan, Timothy H. P.; Lim, Seng Gee; Hong, Wanjin (2004): Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway. In: Journal of Virology 78 (24), S. 14043–14047. DOI: 10.1128/JVI.78.24.14043-14047.2004. </ref> <ref> Tan, Ying-Xim; Tan, Timothy H. P.; Lee, Marvin J-R; Tham, Puay-Yoke; Gunalan, Vithiagaran; Druce, Julian et al. (2007): Induction of apoptosis by the severe acute respiratory syndrome coronavirus 7a protein is dependent on its interaction with the Bcl-XL protein. In: Journal of Virology 81 (12), S. 6346–6355. DOI: 10.1128/JVI.00090-07. </ref> Additionally, interaction of SARS 7a with Ap4A, a hydrolase involved in processes such as cell proliferation, DNA-replication, apoptosis and RNA-processing, leads to downregulation of its hydrolase-activity followed by an increased production of AP4A, which may also contributes to the induction of apoptosis. <ref> Vasilenko, Natalia; Moshynskyy, Igor; Zakhartchouk, Alexander (2010): SARS coronavirus protein 7a interacts with human Ap4A-hydrolase. In: Virol J 7, S. 31. DOI: 10.1186/1743-422X-7-31. </ref> It is also possible that 7a plays a key role in cell cycle control. In HEK 293 cell, an overexpression of 7a led to inhibition of cell growth and induction of the G0/G1 phase cell cycle arrest. This arrest may favour coronavirus replication and exacerbate virus-induced pathogenicity. <ref> Yuan, Xiaoling; Wu, Jie; Shan, Yajun; Yao, Zhenyu; Dong, Bo; Chen, Bo et al. (2006): SARS coronavirus 7a protein blocks cell cycle progression at G0/G1 phase via the cyclin D3/pRb pathway. In: Virology 346 (1), S. 74–85. DOI: 10.1016/j.virol.2005.10.015.
</ref>

== See also ==
[[Coronavirus_Disease 2019 (COVID-19)]]
__NOTOC__
</SX>
== References ==
<references/>

SARS-CoV-2 protein S

2020-04-20T15:14:06Z

Sabrina Staeb:

<SX viewer='molstar' load='' size='340' side='right' caption='' scene=''>
{{Theoretical_model}}
== Function ==
'''Surface glycoprotein (S)'''
Spike protein S1 (residue 14-685): attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 and CLEC4M/DC-SIGNR receptors and internalization of the virus into the endosomes of the host cell induces conformational changes in the S glycoprotein. Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.
Spike protein S2 (residue 686-1273): mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.
Spike protein S2' (residue 816-1273): acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.<ref>[https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref>pmid 32200634</ref>

==Spike Glycoprotein==

The homotrimeric spike glycoprotein on the virus envelope mediates the entry into cell. Every monomer consists of the two subunits S1 and S2. SARS-CoV-2 spike S1 subunit binds the cellular receptor called angiotensin converting enzyme 2 (ACE2). Binding triggers a cascade of events leading to the fusion of cell and virus membrane. After the prefusion trimer is destabilized, the S1 subunit is shedded leading to transition of the S2 subunit to a stable postfusion conformation. To engage a host cell receptor, the receptor-binding domain (RBD) of S1 undergoes hinge-like conformational rearrangement that transiently hide or expose the residues necessary for receptor binding. <ref name="Wrapp"> Wrapp, Daniel; Wang, Nianshuang; Corbett, Kizzmekia S.; Goldsmith, Jory A.; Hsieh, Ching-Lin; Abiona, Olubukola et al. (2020): Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. In: Science 367 (6483), S. 1260–1263. DOI: 10.1126/science.abb2507.</ref>

==Structure Description==

Spike subunits S1 and S2 can be divided into several subdomains. The S1 subunit comprises a signal sequence (SS) on the N-terminal end followed by a N-terminal domain (NTD) and the receptor binding domain (RBD). After two small subdomains (SD1/2), we find two protease cleavage sites (S1/S2 and S2’).The S2 subunit is composed of a fusion peptide (FP), two heptad repeats (HR1 and 2), a central helix (CH), a connector domain (CD), a transmembrane domain (TM) and the cytoplasmic tail (CT). <ref name="Wrapp" />

The structure of the receptor binding domain (RBD), in complex with the human ACE2 receptor, shows that interaction happens via the spike protein RBD and the ACE2 N-terminal peptidase domain. The RBD consists of a twisted five stranded antiparallel β-sheet (β1, β2, β3, β4 und β7) forming the core together with short connecting helices and loops. The spike receptor binding motif (RBM), containing most of the ACE2 contacting residues, is located as an extended insertion between the β4 and β7 strands consisting of short β-sheets (β5 and β6), α-helices (α4 and α5) and loops. The ACE2 N-terminal peptidase domain has two lobes that form the substrate binding site. The contact between RBM and ACE2 is made at the bottom side of the ACE2 small lobe, with a concave outer surface in the RBM accommodating the N-terminal helix of the ACE2 and thus generating an interface of 1687 Å^2. This interface contains a network of different interactions, including hydrophilic interactions with 13 hydrogen bonds and 2 salt bridges. Key residues for for receptor binding include the amino acids Leu544, Phe486, Gln493, and Asn 501. Leu 544 interacts with ACE2 residues Asp30, Lys31 and His34. Phe486, interacts with ACE2 GLN24, Leu79, Met82 (by van der Waals forces) and Tyr 83. Gln 493 forms a hydrogen bond with ACE2 Glu35 and interacts with Lys31 and His34. Another Hydrogen bond is formed between ACE2 Tyr 41 and Asn501 of one α-helix of the RBM. Further, Asn501 also interacts with the amino acid residues Lys353, Gly354 and Asp355. Outside the RBM, there is another unique ACE2-interacting residue Lys417, forming a salt bride with ACE2 Asp30. <ref name="Lan">Lan, Jun; Ge, Jiwan; Yu, Jinfang; Shan, Sisi; Zhou, Huan; Fan, Shilong et al. (2020): Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. In: Nature. DOI: 10.1038/s41586-020-2180-5. </ref> <ref> Yan, Renhong; Zhang, Yuanyuan; Li, Yaning; Xia, Lu; Guo, Yingying; Zhou, Qiang (2020): Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. In: Science 367 (6485), S. 1444–1448. DOI: 10.1126/science.abb2762.
</ref>

==Fusion and Entry Mechanism==

The task of the spike protein is to initiate the fusion and entry with/ into the host cell. A key role in mediating these processes are the domains S-HR1 and S-HR2. The exact mechanism of entry and fusion of SARS-CoV-2 with/ into the host cell is still not fully known but it could be possible that the 2019-nCoV may have similar membrane fusion mechanism as that of SARS-CoV. The putative antiviral mechanism is, that after binding of RBD S1 subunit of 2019-nCoV spike protein to the receptor ACE2 on the host cell, S2 subunit changes conformation by inserting FP into the cell membranes, triggering the association between the HR1 and HR2 domains to form a six-helix-bundle, which brings the viral and cellular membranes in close proximity for fusion.<ref> Xia, Shuai; Zhu, Yun; Liu, Meiqin; Lan, Qiaoshuai; Xu, Wei; Wu, Yanling et al. (2020): Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein. In: Cellular & molecular immunology. DOI: 10.1038/s41423-020-0374-2.</ref>

==Glycosilation of the Spike Protein==

Coronavirus spike proteins are densely decorated by heterogenous N-linked glycans protruding from the trimer surface. SARS-CoV-2 S comprises 22 N-linked glycosylation sequons per protomer. N-linked glycans play a key role in proper protein folding and in priming by host proteases <ref> Walls, Alexandra C.; Park, Young-Jun; Tortorici, M. Alejandra; Wall, Abigail; McGuire, Andrew T.; Veesler, David (2020): Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. In: Cell. DOI: 10.1016/j.cell.2020.02.058.</ref> Since glycans can shield the amino acid residues and other epitopes from cells and antibody recognition, glycosylation can enable the coronavirus to evade both the innate and adaptive immune responses. <ref name="Lan" /> <ref>Shen, Shuo; Tan, Timothy H. P.; Tan, Yee-Joo (2007): Expression, glycosylation, and modification of the spike (S) glycoprotein of SARS CoV. In: Methods in molecular biology (Clifton, N.J.) 379, S. 127–135. DOI: 10.1007/978-1-59745-393-6_9.</ref>

== See also ==
[[Coronavirus_Disease 2019 (COVID-19)]]
__NOTOC__
</SX>
== References ==
<references/>