SMTL ID : 7y59.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-6-mer

Ligands

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain E: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, D.285, I.361, H.365, G.389, A.390 Chain F: R.340 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.188, E:G.188, E:G.229, E:T.230, E:G.231, E:G.231, E:K.232, E:T.233, E:L.234, F:R.340 Salt bridges: E:K.232, E:K.232, F:R.340 ATP.3: 14 residues within 4Å: Chain F: D.186, I.187, G.188, G.229, T.230, G.231, K.232, T.233, L.234, D.285, H.365, G.389, A.390 Chain H: R.340 11 PLIP interactions: 9 interactions with chain F, 2 interactions with chain H Hydrogen bonds: F:G.188, F:G.188, F:G.231, F:K.232, F:T.233, F:T.233, F:L.234, F:D.285, H:R.340 Salt bridges: F:K.232, H:R.340 ATP.5: 17 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, D.285, I.361, H.365, G.389, A.390, A.393 10 PLIP interactions: 9 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:G.188, G:G.229, G:T.230, G:G.231, G:K.232, G:T.233, G:L.234 Salt bridges: G:K.232, G:K.232, E:R.340 ATP.7: 14 residues within 4Å: Chain H: D.186, P.228, G.229, T.230, G.231, K.232, T.233, L.234, D.285, I.361, H.365, G.389, A.390, A.393 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:G.229, H:T.230, H:T.230, H:G.231, H:K.232, H:T.233, H:T.233, H:L.234 Salt bridges: H:K.232, H:K.232 ATP.9: 17 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, D.285, I.361, I.364, H.365, G.389, A.390 17 PLIP interactions: 14 interactions with chain I, 3 interactions with chain G Hydrogen bonds: I:G.188, I:G.188, I:G.229, I:T.230, I:T.230, I:G.231, I:K.232, I:T.233, I:T.233, I:L.234, I:D.285, I:G.389 Salt bridges: I:K.232, I:K.232, G:R.340, G:R.340, G:R.340 ATP.11: 16 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, D.285, I.361, H.365, G.389, A.390 12 PLIP interactions: 11 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:G.188, J:G.188, J:G.229, J:T.230, J:G.231, J:K.232, J:T.233, J:T.233, J:L.234, J:D.285 Salt bridges: J:K.232, I:R.340

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

ADP.2: 15 residues within 4Å: Chain E: D.459, I.460, G.461, P.501, G.502, C.503, G.504, K.505, T.506, L.507, D.558, I.637, A.666, T.669 Chain F: R.616 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:D.459, E:G.461, E:G.502, E:C.503, E:G.504, E:T.506, E:T.506, E:T.506, E:T.669 Salt bridges: E:K.505, E:K.505, F:R.616 ADP.4: 15 residues within 4Å: Chain F: D.459, I.460, P.500, P.501, G.502, C.503, G.504, K.505, T.506, L.507, I.637, G.665, A.666, T.669 Chain H: R.616 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain H Hydrogen bonds: F:D.459, F:G.502, F:C.503, F:G.504, F:K.505, F:T.506, F:T.669, H:R.616 ADP.6: 15 residues within 4Å: Chain G: D.459, I.460, G.461, P.501, G.502, C.503, G.504, K.505, T.506, L.507, D.558, N.605, I.637, A.666, T.669 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:D.459, G:G.461, G:G.502, G:C.503, G:G.504, G:K.505, G:T.506, G:N.605, G:N.605, G:T.669 ADP.8: 12 residues within 4Å: Chain H: D.459, I.460, G.502, C.503, G.504, K.505, T.506, L.507, I.637, N.641, G.665, A.666 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:G.502, H:G.504, H:K.505, H:T.506, H:N.641, H:N.641, H:G.665 ADP.10: 16 residues within 4Å: Chain G: R.616 Chain I: D.459, I.460, P.500, P.501, G.502, C.503, G.504, K.505, T.506, L.507, D.558, I.637, A.640, G.665, A.666 11 PLIP interactions: 10 interactions with chain I, 1 interactions with chain G Hydrogen bonds: I:D.459, I:P.500, I:G.502, I:C.503, I:G.504, I:K.505, I:T.506, I:S.664, G:R.616 Salt bridges: I:K.505, I:K.505 ADP.12: 14 residues within 4Å: Chain I: R.616 Chain J: D.459, I.460, P.501, G.502, C.503, G.504, K.505, T.506, L.507, D.558, I.637, G.665, A.666 9 PLIP interactions: 8 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:D.459, J:G.461, J:G.502, J:C.503, J:G.504, J:K.505, J:T.506, J:A.666 Salt bridges: I:R.616

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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