SMTL ID : 9llk.1

The cryo-EM structure of the heterododecameric human Derlin-1/p97 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: 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.390 Chain B: R.340 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.188, A:G.188, A:G.229, A:T.230, A:G.231, A:K.232, A:T.233 Salt bridges: B:R.340 ADP.2: 11 residues within 4Å: Chain A: I.460, G.461, G.502, C.503, G.504, K.505, T.506, L.507, G.665, A.666, T.669 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.461, A:G.461, A:G.502, A:G.504, A:K.505, A:T.506, A:D.558 Salt bridges: A:K.505 ADP.3: 15 residues within 4Å: Chain B: 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 I: R.340 10 PLIP interactions: 1 interactions with chain I, 9 interactions with chain B Salt bridges: I:R.340, B:K.232 Hydrogen bonds: B:G.188, B:G.188, B:G.229, B:T.230, B:G.231, B:K.232, B:T.233, B:L.234 ADP.4: 11 residues within 4Å: Chain B: I.460, G.461, P.501, G.502, C.503, G.504, K.505, T.506, L.507, G.665, T.669 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.461, B:G.461, B:G.502, B:C.503, B:G.504, B:K.505, B:T.506, B:T.506, B:T.506, B:L.507 Salt bridges: B:K.505 ADP.5: 10 residues within 4Å: Chain E: I.187, G.188, G.229, T.230, G.231, K.232, T.233, I.361, H.365, G.389 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.188, E:G.188, E:G.229, E:T.230, E:G.231, E:K.232, E:T.233, F:R.340 ADP.6: 11 residues within 4Å: Chain E: I.460, G.461, G.502, C.503, G.504, K.505, T.506, I.637, G.665, A.666, 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:D.558 Salt bridges: E:K.505 ADP.7: 14 residues within 4Å: Chain A: R.340 Chain F: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, I.361, H.365, G.389, A.393 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.188, F:G.188, F:G.229, F:G.231, F:K.232, F:T.233 Salt bridges: F:K.232, A:R.340 ADP.8: 11 residues within 4Å: Chain F: I.460, G.461, G.502, C.503, G.504, K.505, T.506, L.507, G.665, A.666, T.669 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:G.461, F:G.461, F:G.502, F:C.503, F:G.504, F:K.505, F:T.506, F:T.506 Salt bridges: F:K.505 ADP.9: 14 residues within 4Å: Chain I: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, I.361, H.365, G.389, A.393 Chain J: R.340 9 PLIP interactions: 8 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:G.188, I:G.188, I:G.229, I:T.230, I:G.231, I:K.232, I:T.233 Salt bridges: I:K.232, J:R.340 ADP.10: 11 residues within 4Å: Chain I: D.459, I.460, G.461, G.502, C.503, G.504, K.505, T.506, G.665, A.666, T.669 8 PLIP interactions: 8 interactions with chain I Hydrogen bonds: I:G.461, I:G.461, I:G.502, I:C.503, I:G.504, I:K.505, I:T.506 Salt bridges: I:K.505 ADP.11: 14 residues within 4Å: Chain E: R.340 Chain J: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, I.361, H.365, G.389, A.393 9 PLIP interactions: 8 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:G.188, J:G.188, J:G.229, J:T.230, J:G.231, J:K.232, J:T.233 Salt bridges: J:K.232, E:R.340 ADP.12: 13 residues within 4Å: Chain J: I.460, G.461, G.502, C.503, G.504, K.505, T.506, L.507, I.637, N.641, G.665, A.666, T.669 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:G.461, J:G.461, J:G.502, J:C.503, J:G.504, J:K.505, J:T.506, J:T.506, J:T.506, J:L.507, J:N.641 Salt bridges: J:K.505

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., Cryo-EM structure of the human Derlin-1/p97 complex reveals a hexameric channel in ERAD. Commun Biol (2025)

Release Date

2025-10-29

Peptides

Transitional endoplasmic reticulum ATPase: ABEFIJ
Derlin-1: CDGHKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

E
F

F
A

I
D

J
E

C
V

D
W

G
Z

H
U

K
X

L
Y

Membrane

We predict this structure to be a membrane protein.
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Transitional endoplasmic reticulum ATPase

Derlin-1

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