SMTL ID : 8t2v.1

Cryo-EM Structures of Full-length Integrin alphaIIbbeta3 in Native Lipids

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: H.798, W.929, N.931, R.946 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: W.262, R.281, M.285 Chain B: N.316, L.317, N.320 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA.3: 5 residues within 4Å: Chain B: N.99, N.371, P.381, S.398 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 4 residues within 4Å: Chain B: K.98, N.99 Ligands: NAG-NAG-BMA-BMA-BMA.3, NAG-NAG-BMA-BMA-BMA.3 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-BMA.5: 4 residues within 4Å: Chain B: N.449, N.450, N.452, W.466 No protein-ligand interaction detected (PLIP)

7 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: D.297, N.299, D.301, R.303, D.305, L.332 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.301, A:D.301, A:R.303, A:D.305, A:D.305 CA.7: 6 residues within 4Å: Chain A: E.243, D.245, D.247, T.250, T.251, E.252 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.243, A:D.245, A:D.247, A:T.250, A:T.250 CA.8: 8 residues within 4Å: Chain A: D.365, L.366, D.367, D.369, Y.371, D.373, L.393, G.394 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.367, A:D.369, A:D.369, A:Y.371, A:D.373 CA.9: 6 residues within 4Å: Chain A: D.426, D.428, N.430, Y.432, D.434, A.450 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.428, A:Y.432, A:D.434 CA.14: 7 residues within 4Å: Chain A: C.602, G.603, D.605, V.607, C.608, V.609, E.642 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.602, A:D.605, A:D.605, A:V.607, A:E.642 CA.19: 5 residues within 4Å: Chain B: D.158, N.215, D.217, P.219, E.220 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.158, B:D.217, B:D.217, B:P.219, B:E.220 CA.20: 6 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, M.335, D.336 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:D.127, B:M.335, H2O.1, H2O.1

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.10: 2 residues within 4Å: Chain A: L.248, N.249 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.248 Hydrogen bonds: A:N.249 NAG.11: 2 residues within 4Å: Chain A: E.679, N.680 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain A: E.507, N.570, T.590, H.591 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.570, A:T.590 NAG.13: 1 residues within 4Å: Chain A: N.15 No protein-ligand interaction detected (PLIP) NAG.15: 9 residues within 4Å: Chain B: K.646, D.647, T.648, G.649, A.652, V.653, N.654, Q.668, Y.669 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.652, B:Q.668 Hydrogen bonds: B:D.647, B:N.654 NAG.21: 3 residues within 4Å: Chain B: Y.531, N.559, C.560 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.531

2 x CLR: CHOLESTEROL(Non-functional Binders)

CLR.16: 1 residues within 4Å: Chain B: I.714 No protein-ligand interaction detected (PLIP) CLR.17: 3 residues within 4Å: Chain B: L.694, L.697, M.701 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.18: 3 residues within 4Å: Chain B: S.121, N.215, E.220 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.121, H2O.1, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adair, B.D. et al., Cryo-EM structures of full-length integrin alpha IIb beta 3 in native lipids. Nat Commun (2023)

Release Date

2023-07-26

Peptides

Integrin alpha-IIb: A
Integrin beta-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Integrin alpha-IIb

Integrin beta-3

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