SMTL ID : 8t2v.1

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

Coordinates

PDB Format

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

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: W.929, F.930, N.931 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain B: N.316, L.317, N.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.281

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

NAG-NAG.2: 3 residues within 4Å: Chain B: Y.531, Y.557, N.559 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.99 Ligands: NAG-NAG-BMA-BMA-BMA.4 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.4: 4 residues within 4Å: Chain B: N.99, N.371, S.398 Ligands: NAG-NAG.5 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

NAG-NAG-BMA-BMA.6: 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.7: 5 residues within 4Å: Chain A: D.297, N.299, D.301, R.303, D.305 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.297, A:D.301, A:D.301, A:R.303, A:D.305 CA.8: 5 residues within 4Å: Chain A: E.243, D.245, D.247, T.250, E.252 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.243, A:D.247, A:T.250, A:E.252, A:E.252 CA.9: 5 residues within 4Å: Chain A: D.365, D.367, D.369, Y.371, D.373 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.367, A:D.369, A:Y.371, A:D.373, A:D.373 CA.10: 5 residues within 4Å: Chain A: D.426, D.428, N.430, Y.432, D.434 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.428, A:D.428, A:Y.432, A:D.434, A:D.434 CA.15: 4 residues within 4Å: Chain A: C.602, D.605, V.607, E.642 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.602, A:D.605, A:V.607, A:E.642, A:E.642 CA.20: 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.21: 4 residues within 4Å: Chain B: S.123, D.126, D.127, M.335 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.123, B:D.126, B:D.127, B:M.335, H2O.1

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

NAG.11: 2 residues within 4Å: Chain A: L.248, N.249 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.248 NAG.12: 2 residues within 4Å: Chain A: E.679, N.680 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain A: E.507, N.570, T.590 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.590 NAG.14: 1 residues within 4Å: Chain A: N.15 No protein-ligand interaction detected (PLIP) NAG.16: 7 residues within 4Å: Chain B: L.645, K.646, D.647, A.652, V.653, N.654, Q.668 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.652, B:Q.668 Hydrogen bonds: B:K.646, B:D.647, B:N.654

2 x CLR: CHOLESTEROL(Non-functional Binders)

CLR.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CLR.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.19: 2 residues within 4Å: Chain B: S.121, 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.
Show / Hide

Integrin alpha-IIb

Integrin beta-3

Related Entries With Identical Sequence