SMTL ID : 9dil.1

Cryo-EM structure of VCP/p97 in complex with VCPIP1 (VCIP135)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-2-1-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: D.205, I.206, G.207, G.208, P.247, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.207, A:G.207, A:G.248, A:T.249, A:T.249, A:G.250, A:K.251, A:T.252, A:L.253 Salt bridges: A:K.251 ADP.2: 12 residues within 4Å: Chain A: D.478, I.479, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.521, A:C.522, A:C.522, A:G.523, A:K.524, A:T.525, A:T.525, A:T.525, A:L.526, A:T.688 Salt bridges: A:K.524 ADP.3: 15 residues within 4Å: Chain A: R.359 Chain B: D.205, I.206, G.207, G.208, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.207, B:G.208, B:G.248, B:T.249, B:G.250, B:K.251, B:T.252, B:L.253, A:R.359 Salt bridges: B:K.251, A:R.359 ADP.4: 13 residues within 4Å: Chain B: D.478, I.479, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.521, B:C.522, B:C.522, B:G.523, B:K.524, B:T.525, B:T.525, B:T.525, B:G.684 Salt bridges: B:K.524

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vostal, L.E. et al., Structural insights into the coupling between VCP, an essential unfoldase, and a deubiquitinase. J.Cell Biol. (2025)

Release Date

2025-03-26

Peptides

Transitional endoplasmic reticulum ATPase: AB
Deubiquitinating protein VCPIP1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Transitional endoplasmic reticulum ATPase

Deubiquitinating protein VCPIP1

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