SMTL ID : 7nwl.1

Cryo-EM structure of human integrin alpha5beta1 (open form) in complex with fibronectin and TS2/16 Fv-clasp

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

4 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: P.15, N.43, L.50 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 1 residues within 4Å: Chain A: N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain A: E.504, N.568, R.593 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain B: N.343, S.345 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 2 residues within 4Å: Chain A: N.256, S.277 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: K.382, N.397 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-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-MAN-MAN.4: 5 residues within 4Å: Chain A: D.243, N.266, S.268, D.269, L.273 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-NAG-MAN.5: 8 residues within 4Å: Chain A: R.220, A.222, S.223, Y.226, Y.261, S.272, N.275 Chain C: I.197 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:I.197, A:A.222

1 x NAG- NAG- BMA- MAN: alpha-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-MAN.9: 3 residues within 4Å: Chain B: Y.380, G.384, N.386 No protein-ligand interaction detected (PLIP)

7 x MN: MANGANESE (II) ION(Non-covalent)

MN.11: 5 residues within 4Å: Chain A: E.239, S.241, D.243, T.245, D.247 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.239, A:S.241, A:D.243, A:T.245, A:D.247 MN.12: 5 residues within 4Å: Chain A: D.293, N.295, D.297, L.299, D.301 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.293, A:D.297, A:L.299, A:D.301, A:D.301 MN.13: 6 residues within 4Å: Chain A: D.360, D.362, D.364, Y.366, D.368, G.389 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.360, A:D.362, A:D.364, A:Y.366, A:D.368 MN.14: 5 residues within 4Å: Chain A: D.424, D.426, N.428, Y.430, D.432 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.424, A:D.426, A:Y.430, A:D.432 MN.15: 6 residues within 4Å: Chain B: S.132, S.134, E.229, D.259, A.260 Chain C: D.354 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:S.132, B:S.134, B:E.229, C:D.354 MN.16: 5 residues within 4Å: Chain B: S.134, D.137, D.138, D.259 Chain C: Y.305 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.134, B:D.137, B:D.138, B:D.259 MN.17: 5 residues within 4Å: Chain B: E.169, N.224, D.226, P.228, E.229 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.169, B:D.226, B:P.228, B:E.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schumacher, S. et al., Structural insights into integrin alpha 5 beta 1 opening by fibronectin ligand. Sci Adv (2021)

Release Date

2021-06-02

Peptides

Integrin alpha-5: A
Integrin beta-1: B
Isoform 1 of Fibronectin: C
TS2/16 VH(S112C)-SARAH Chimera: D
TS2/16 VL-SARAH(S37C) Chimera: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Integrin alpha-5

Integrin beta-1

Isoform 1 of Fibronectin

TS2/16 VH(S112C)-SARAH Chimera

TS2/16 VL-SARAH(S37C) Chimera

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