SMTL ID : 7y53.1

The cryo-EM structure of human ERAD retro-translocation complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-6-mer

Ligands

12 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 12 residues within 4Å: Chain E: D.186, I.187, G.188, G.229, T.230, G.231, K.232, T.233, D.285, H.365, G.389 Chain F: R.340 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.188, E:G.188, E:G.229, E:G.231, E:K.232, E:T.233, E:D.285, F:R.340 Salt bridges: E:K.232, F:R.340 ADP.2: 12 residues within 4Å: Chain E: D.459, I.460, G.461, G.502, C.503, G.504, K.505, T.506, L.507, I.637, G.665, T.669 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.461, E:G.461, E:G.502, E:C.503, E:G.504, E:K.505, E:T.506, E:T.506 Salt bridges: E:K.505 ADP.3: 15 residues within 4Å: Chain F: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, I.361, H.365, G.389, A.393 Chain H: R.340 10 PLIP interactions: 1 interactions with chain H, 9 interactions with chain F Salt bridges: H:R.340, F:K.232 Hydrogen bonds: F:G.188, F:G.188, F:G.229, F:T.230, F:G.231, F:K.232, F:T.233, F:L.234 ADP.4: 14 residues within 4Å: Chain F: D.459, I.460, G.461, P.501, G.502, C.503, G.504, K.505, T.506, L.507, I.637, G.665, T.669 Chain H: R.616 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain H Hydrogen bonds: F:D.459, F:G.461, F:G.502, F:C.503, F:G.504, F:K.505, F:T.506, F:T.506, F:T.506, F:L.507, F:T.669, H:R.616 Salt bridges: F:K.505 ADP.5: 15 residues within 4Å: Chain E: R.340 Chain G: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, I.361, H.365, G.389, A.393 11 PLIP interactions: 9 interactions with chain G, 2 interactions with chain E Hydrogen bonds: G:G.188, G:G.188, G:G.229, G:T.230, G:G.231, G:K.232, G:T.233, G:T.233, E:R.340 Salt bridges: G:K.232, E:R.340 ADP.6: 14 residues within 4Å: Chain G: I.460, G.461, P.501, G.502, C.503, G.504, K.505, T.506, L.507, I.637, N.641, G.665, A.666, T.669 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:G.461, G:G.502, G:G.504, G:K.505, G:T.506, G:T.506, G:T.506, G:L.507, G:N.641 Salt bridges: G:K.505 ADP.7: 14 residues within 4Å: Chain H: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, H.365, G.389, A.393 Chain J: R.340 8 PLIP interactions: 7 interactions with chain H, 1 interactions with chain J Hydrogen bonds: H:G.188, H:G.188, H:G.229, H:G.231, H:K.232, H:T.233 Salt bridges: H:K.232, J:R.340 ADP.8: 14 residues within 4Å: Chain H: D.459, I.460, G.461, G.502, C.503, G.504, K.505, T.506, L.507, I.637, N.641, G.665, T.669 Chain J: R.616 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain J Hydrogen bonds: H:G.461, H:G.461, H:G.502, H:C.503, H:G.504, H:K.505, H:T.506, H:N.641, J:R.616 Salt bridges: H:K.505 ADP.9: 14 residues within 4Å: Chain G: R.340 Chain I: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, H.365, G.389, A.393 9 PLIP interactions: 8 interactions with chain I, 1 interactions with chain G Hydrogen bonds: I:G.188, I:G.188, I:G.229, I:T.230, I:G.231, I:K.232, I:T.233, G:R.340 Salt bridges: I:K.232 ADP.10: 13 residues within 4Å: Chain I: D.459, I.460, G.461, P.501, G.502, C.503, G.504, K.505, T.506, L.507, I.637, G.665, T.669 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:D.459, I:G.461, I:G.502, I:C.503, I:G.504, I:K.505, I:T.506, I:T.506, I:T.506, I:T.669 Salt bridges: I:K.505, I:K.505 ADP.11: 15 residues within 4Å: Chain I: R.340 Chain J: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, I.361, H.365, G.389, A.393 9 PLIP interactions: 7 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:G.188, J:G.188, J:G.229, J:G.231, J:K.232, J:T.233, I:R.340 Salt bridges: J:K.232, I:R.340 ADP.12: 13 residues within 4Å: Chain J: D.459, I.460, G.461, G.502, C.503, K.505, T.506, L.507, D.558, I.637, N.641, G.665, T.669 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:D.459, J:G.461, J:G.502, J:K.505, J:T.506, J:T.506, J:N.641, J:T.669 Salt bridges: J:K.505

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rao, B. et al., The cryo-EM structure of the human ERAD retrotranslocation complex. Sci Adv (2023)

Release Date

2023-10-18

Peptides

Derlin-1: ABCD
Transitional endoplasmic reticulum ATPase: EFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
W

B
X

C
Y

D
Z

E
A

F
B

G
C

H
D

I
E

J
F

Derlin-1

Transitional endoplasmic reticulum ATPase

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