Sandbox Reserved 1493: Difference between revisions

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=== αIIb subunit ===

The '''αIIb subunit''' (glycoprotein IIb) is composed of 1008 amino acids unevenly distributed over 2 chains. A part forms a light chain which comports a cytoplasmic tail of 20 amino acids and a transmembrane helix. An extracellular disulfide segment links this chain to the <scene name='80/802667/Alpha_head/1'>heavy extracellular domain</scene> which is part of the headpiece of the integrin.

The '''αIIb subunit''' (glycoprotein IIb) is composed of 1008 amino acids unevenly distributed over 2 chains. A part forms a light chain which comports a cytoplasmic tail of 20 amino acids and a transmembrane helix. An extracellular disulfide segment links this chain to the <scene name='80/802667/Alpha_head/3'>heavy extracellular domain</scene> which is part of the headpiece of the integrin.

The extracellular N-Terminus forms a cap over the '''β-propeller''' domain which is folded by seven successive blades of aminoterminal repeats. Each blade is a β-hairpin loop-like structure composed of 4 antiparallel β strands located in each repeat and connected by loops of the surface. This β-propeller is linked to a '''thigh''' and '''two calf''' domains, which form the leg structure that supports the heavy head. The total forms the stalk of the αIIb subunit. The knee of the subunit between the thigh and the first calf domain is the site at which the head bends (inactivated form of the integrin.

The β-propeller hosts multiple '''cation biding sites'''. The last 3 or 4 blades bind <scene name='80/802667/Ca_ions_on_beta-propeller/3'>Ca2+ ions</scene> which influence ligand binding on the lower side of the blades and play an important role in biogenesis and stability of the heterodimer. The '''I domain''' inserted between blades 2 and 3 in the β-propeller follows a Rossman fold with five β-sheets surrounded by seven α-helices. Ligand binding occurs between the β-propeller and the β I domain of the β3 subunit via a coordinating '''Mg2+ ion''' in the MIDAS of the β3 subunit.

The β-propeller hosts multiple '''cation biding sites'''. The last 3 or 4 blades bind <scene name='80/802667/Ca_ions_on_beta-propeller/4'>Ca2+ ions</scene> which influence ligand binding on the lower side of the blades and play an important role in biogenesis and stability of the heterodimer. The '''I domain''' inserted between blades 2 and 3 in the β-propeller follows a Rossman fold with five β-sheets surrounded by seven α-helices. Ligand binding occurs between the β-propeller and the β I domain of the β3 subunit via a coordinating '''Mg2+ ion''' in the MIDAS of the β3 subunit.

The '''RGD binding site''' (Arg-Gly-Asp) is in a crevice in this region, inserted between the β-propeller and β I domains.

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The β3 subunit (glycoprotein IIIa) is a 762 amino acids polypeptide chain.

Its <scene name='80/802667/Beta_head/1'>head</scene> is composed of a '''β I domain''' which has a fold similar to the I domain of the head of the α subunit. Is has a <scene name='80/802667/Mg_in_beta_head_midas/2'>Mg2+</scene> coordinating '''metal ion dependent adhesion site (MIDAS)''' motif and a site adjacent to MIDAS ('''ADMIDAS''') which coordinates ions and plays a part in activity modulation.

Its <scene name='80/802667/Beta_head/2'>head</scene> is composed of a '''β I domain''' which has a fold similar to the I domain of the head of the α subunit. Is has a <scene name='80/802667/Mg_in_beta_head_midas/2'>Mg2+</scene> coordinating '''metal ion dependent adhesion site (MIDAS)''' motif and a site adjacent to MIDAS ('''ADMIDAS''') which coordinates ions and plays a part in activity modulation. In the head can be found the RGD and KGD binding sites.

Its '''stalk''' is mainly composed of a plexin-sempahorin-integrin (PSI) domain and a '''hybrid domain'''. A '''cysteine-rich core''' occupies the extracellular part of β3 from residues 400 to 650. ~~It is linked to~~ the N-terminal of the protein thanks to a long-range disulfide bond. ~~As the globular head is part of the ligand-binding headpiece~~ (~~1 cation binding site~~, ~~RGD and KGD binding sites~~), the ~~cysteine-rich region is~~ thought to have a role in the activation of the headpiece.

Its '''stalk''' is mainly composed of a plexin-sempahorin-integrin (PSI) domain and a '''hybrid domain'''. A '''cysteine-rich core''' occupies the extracellular part of β3 from residues 400 to 650. Other cysteins links the N-terminal of the protein to the β I domain thanks to a long-range disulfide bond. <scene name='80/802667/Beta_head_cysteines/1'>Cysteines</scene> ''(displayed in purple, disulfide bonds in yellow)'' of the extracellular domain the β subunit are thought to have a role in the activation of the headpiece.

The cytoplasmic tail of the β3 subunit has a NPLY domain which binds proteins with phosphotyrosine binding (PTB) domains.

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=== Cation binding sites ===

Multiple '''cation binding sites''' of integrin are located in the head of both subunits and are indirectly involved in ligand binding. <scene name='80/802667/Ca_ions_on_beta-propeller/3'>Calcium ions</scene> in αIIb coordinate '''EF-hand patterns''' (helix-loop-helix calcium binding patterns forming the blades of the β-propeller) which contribute to the structure of the active site and influence ligand binding.

Multiple '''cation binding sites''' of integrin are located in the head of both subunits and are indirectly involved in ligand binding. <scene name='80/802667/Ca_ions_on_beta-propeller/4'>Calcium ions</scene> in αIIb coordinate '''EF-hand patterns''' (helix-loop-helix calcium binding patterns forming the blades of the β-propeller) which contribute to the structure of the active site and influence ligand binding.

The β I domain which also interacts with the ligand includes 3 metal ion binding sites: a <scene name='80/802667/Mg_in_beta_head_midas/2'>Mg2+</scene> ion in '''MIDAS''' surrounded by 2 Ca2+ ions (including one from AMIDAS). MIDAS Mg2+ ion coordinates the Asp side chain of ligands containing RGD.

Sandbox Reserved 1493: Difference between revisions

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@@ Line 23: / Line 23: @@
 === αIIb subunit ===
-The '''αIIb subunit''' (glycoprotein IIb) is composed of 1008 amino acids unevenly distributed over 2 chains. A part forms a light chain which comports a cytoplasmic tail of 20 amino acids and a transmembrane helix. An extracellular disulfide segment links this chain to the <scene name='80/802667/Alpha_head/1'>heavy extracellular domain</scene> which is part of the headpiece of the integrin.
+The '''αIIb subunit''' (glycoprotein IIb) is composed of 1008 amino acids unevenly distributed over 2 chains. A part forms a light chain which comports a cytoplasmic tail of 20 amino acids and a transmembrane helix. An extracellular disulfide segment links this chain to the <scene name='80/802667/Alpha_head/3'>heavy extracellular domain</scene> which is part of the headpiece of the integrin.
 The extracellular N-Terminus forms a cap over the '''β-propeller''' domain which is folded by seven successive blades of aminoterminal repeats. Each blade is a β-hairpin loop-like structure composed of 4 antiparallel β strands located in each repeat and connected by loops of the surface. This β-propeller is linked to a '''thigh''' and '''two calf''' domains, which form the leg structure that supports the heavy head. The total forms the stalk of the αIIb subunit. The knee of the subunit between the thigh and the first calf domain is the site at which the head bends (inactivated form of the integrin.
-The β-propeller hosts multiple '''cation biding sites'''. The last 3 or 4 blades bind <scene name='80/802667/Ca_ions_on_beta-propeller/3'>Ca2+ ions</scene> which influence ligand binding on the lower side of the blades and play an important role in biogenesis and stability of the heterodimer. The '''I domain''' inserted between blades 2 and 3 in the β-propeller follows a Rossman fold with five β-sheets surrounded by seven α-helices. Ligand binding occurs between the β-propeller and the β I domain of the β3 subunit via a coordinating '''Mg2+ ion''' in the MIDAS of the β3 subunit.
+The β-propeller hosts multiple '''cation biding sites'''. The last 3 or 4 blades bind <scene name='80/802667/Ca_ions_on_beta-propeller/4'>Ca2+ ions</scene> which influence ligand binding on the lower side of the blades and play an important role in biogenesis and stability of the heterodimer. The '''I domain''' inserted between blades 2 and 3 in the β-propeller follows a Rossman fold with five β-sheets surrounded by seven α-helices. Ligand binding occurs between the β-propeller and the β I domain of the β3 subunit via a coordinating '''Mg2+ ion''' in the MIDAS of the β3 subunit.
 The '''RGD binding site''' (Arg-Gly-Asp) is in a crevice in this region, inserted between the β-propeller and β I domains.
@@ Line 35: / Line 35: @@
 The β3 subunit (glycoprotein IIIa) is a 762 amino acids polypeptide chain.
-Its <scene name='80/802667/Beta_head/1'>head</scene> is composed of a '''β I domain''' which has a fold similar to the I domain of the head of the α subunit. Is has a <scene name='80/802667/Mg_in_beta_head_midas/2'>Mg2+</scene> coordinating '''metal ion dependent adhesion site (MIDAS)''' motif and a site adjacent to MIDAS ('''ADMIDAS''') which coordinates ions and plays a part in activity modulation.
+Its <scene name='80/802667/Beta_head/2'>head</scene> is composed of a '''β I domain''' which has a fold similar to the I domain of the head of the α subunit. Is has a <scene name='80/802667/Mg_in_beta_head_midas/2'>Mg2+</scene> coordinating '''metal ion dependent adhesion site (MIDAS)''' motif and a site adjacent to MIDAS ('''ADMIDAS''') which coordinates ions and plays a part in activity modulation. In the head can be found the RGD and KGD binding sites.
-Its '''stalk''' is mainly composed of a plexin-sempahorin-integrin (PSI) domain and a '''hybrid domain'''. A '''cysteine-rich core''' occupies the extracellular part of β3 from residues 400 to 650. It is linked to the N-terminal of the protein thanks to a long-range disulfide bond. As the globular head is part of the ligand-binding headpiece (1 cation binding site, RGD and KGD binding sites), the cysteine-rich region is thought to have a role in the activation of the headpiece.
+Its '''stalk''' is mainly composed of a plexin-sempahorin-integrin (PSI) domain and a '''hybrid domain'''. A '''cysteine-rich core''' occupies the extracellular part of β3 from residues 400 to 650. Other cysteins links the N-terminal of the protein to the β I domain thanks to a long-range disulfide bond. <scene name='80/802667/Beta_head_cysteines/1'>Cysteines</scene> ''(displayed in purple, disulfide bonds in yellow)'' of the extracellular domain the β subunit are thought to have a role in the activation of the headpiece.
 The cytoplasmic tail of the β3 subunit has a NPLY domain which binds proteins with phosphotyrosine binding (PTB) domains.
@@ Line 53: / Line 53: @@
 === Cation binding sites ===
-Multiple '''cation binding sites''' of integrin are located in the head of both subunits and are indirectly involved in ligand binding. <scene name='80/802667/Ca_ions_on_beta-propeller/3'>Calcium ions</scene> in αIIb coordinate '''EF-hand patterns''' (helix-loop-helix calcium binding patterns forming the blades of the β-propeller) which contribute to the structure of the active site and influence ligand binding.
+Multiple '''cation binding sites''' of integrin are located in the head of both subunits and are indirectly involved in ligand binding. <scene name='80/802667/Ca_ions_on_beta-propeller/4'>Calcium ions</scene> in αIIb coordinate '''EF-hand patterns''' (helix-loop-helix calcium binding patterns forming the blades of the β-propeller) which contribute to the structure of the active site and influence ligand binding.
 The β I domain which also interacts with the ligand includes 3 metal ion binding sites: a <scene name='80/802667/Mg_in_beta_head_midas/2'>Mg2+</scene> ion in '''MIDAS''' surrounded by 2 Ca2+ ions (including one from AMIDAS). MIDAS Mg2+ ion coordinates the Asp side chain of ligands containing RGD.