SMTL ID : 8jp7.1

Cryo-EM structure of the head region of full-length ERGIC-53 with MCFD2 (Substate B)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

16 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.152, F.154, N.156, D.181 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.152, A:D.152, A:F.154, A:D.181 CA.2: 5 residues within 4Å: Chain A: D.155, D.157, N.161, N.162, D.181 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.155, A:D.157, A:D.157, A:D.181 CA.3: 4 residues within 4Å: Chain B: D.152, F.154, N.156, D.181 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.152, B:D.152, B:F.154, B:D.181 CA.4: 5 residues within 4Å: Chain B: D.155, D.157, N.161, N.162, D.181 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.155, B:D.157, B:D.157, B:D.181 CA.5: 6 residues within 4Å: Chain C: D.107, N.109, D.111, Y.113, D.115, E.118 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.107, C:D.111, C:Y.113, C:D.115, C:E.118 CA.6: 6 residues within 4Å: Chain C: D.59, D.61, N.63, L.65, D.67, E.70 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.59, C:D.61, C:L.65, C:E.70, C:E.70 CA.8: 5 residues within 4Å: Chain D: D.107, N.109, D.111, Y.113, E.118 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.107, D:D.111, D:D.111, D:Y.113, D:E.118 CA.9: 6 residues within 4Å: Chain D: D.59, D.61, N.63, L.65, D.67, E.70 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.59, D:D.61, D:D.61, D:L.65, D:E.70 CA.11: 5 residues within 4Å: Chain E: D.121, D.152, F.154, N.156, D.181 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.152, E:D.152, E:F.154, E:D.181 CA.12: 5 residues within 4Å: Chain E: D.155, D.157, N.161, N.162, D.181 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.155, E:D.157, E:D.157, E:D.181 CA.13: 6 residues within 4Å: Chain F: D.107, N.109, D.111, Y.113, D.115, E.118 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.107, F:D.111, F:Y.113, F:D.115, F:E.118 CA.14: 5 residues within 4Å: Chain F: D.59, D.61, N.63, L.65, E.70 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.59, F:D.61, F:L.65, F:E.70, F:E.70 CA.16: 5 residues within 4Å: Chain G: D.107, N.109, D.111, Y.113, E.118 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.107, G:D.111, G:D.111, G:Y.113, G:E.118 CA.17: 6 residues within 4Å: Chain G: D.59, D.61, N.63, L.65, D.67, E.70 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.59, G:D.61, G:D.61, G:L.65, G:E.70 CA.19: 4 residues within 4Å: Chain H: D.152, F.154, N.156, D.181 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.152, H:D.152, H:F.154, H:D.181 CA.20: 5 residues within 4Å: Chain H: D.155, D.157, N.161, N.162, D.181 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.155, H:D.157, H:D.157, H:D.181

4 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain C: H.29, H.33, H.77, H.79 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.29, C:H.33, C:H.77, C:H.79 ZN.10: 4 residues within 4Å: Chain D: H.29, H.33, H.77, H.79 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.29, D:H.33, D:H.77, D:H.79 ZN.15: 4 residues within 4Å: Chain F: H.29, H.33, H.77, H.79 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.29, F:H.33, F:H.77, F:H.79 ZN.18: 4 residues within 4Å: Chain G: H.29, H.33, H.77, H.79 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:H.29, G:H.29, G:H.33, G:H.77, G:H.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, S. et al., Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport. Nat Commun (2024)

Release Date

2024-04-17

Peptides

Protein ERGIC-53: ABEH
Multiple coagulation factor deficiency protein 2: CDFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

H
F

C
C

D
D

F
G

G
H

Protein ERGIC-53

Multiple coagulation factor deficiency protein 2

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