SMTL ID : 8fcn.1

Cryo-EM structure of p97:UBXD1 VIM-only state

Coordinates

PDB Format

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 B: D.205, I.206, G.207, G.208, G.248, T.249, G.250, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain D: F.360 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.207, B:G.208, B:G.248, B:T.249, B:T.252, B:L.253, B:D.304 ADP.2: 15 residues within 4Å: Chain B: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.480, B:G.521, B:C.522, B:G.523, B:K.524, B:T.525, B:T.525, B:T.525, B:L.526, B:N.660, B:T.688 Salt bridges: B:K.524 ADP.3: 15 residues within 4Å: Chain D: D.205, I.206, G.207, G.208, G.248, T.249, G.250, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain F: F.360 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.207, D:G.208, D:G.248, D:T.249, D:T.252, D:L.253, D:D.304 ADP.4: 15 residues within 4Å: Chain D: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.480, D:G.521, D:C.522, D:G.523, D:K.524, D:T.525, D:T.525, D:T.525, D:L.526, D:N.660, D:T.688 Salt bridges: D:K.524 ADP.5: 16 residues within 4Å: Chain F: D.205, I.206, G.207, G.208, P.247, G.248, T.249, G.250, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain H: F.360 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.207, F:G.208, F:G.248, F:T.249, F:T.252, F:L.253, F:D.304 ADP.6: 15 residues within 4Å: Chain F: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.480, F:G.480, F:G.521, F:G.523, F:K.524, F:T.525, F:T.525, F:T.525, F:L.526, F:N.660, F:T.688 Salt bridges: F:K.524 ADP.7: 16 residues within 4Å: Chain H: D.205, I.206, G.207, G.208, P.247, G.248, T.249, G.250, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain J: F.360 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:G.207, H:G.208, H:G.248, H:T.249, H:T.252, H:L.253, H:D.304 ADP.8: 15 residues within 4Å: Chain H: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:G.480, H:G.521, H:C.522, H:G.523, H:K.524, H:T.525, H:T.525, H:T.525, H:L.526, H:N.660, H:T.688 Salt bridges: H:K.524 ADP.9: 16 residues within 4Å: Chain J: D.205, I.206, G.207, G.208, P.247, G.248, T.249, G.250, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain L: F.360 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:G.207, J:G.208, J:G.248, J:T.249, J:T.252, J:L.253, J:D.304 ADP.10: 15 residues within 4Å: Chain J: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:G.480, J:G.480, J:G.521, J:G.523, J:K.524, J:T.525, J:T.525, J:T.525, J:L.526, J:N.660, J:T.688 Salt bridges: J:K.524 ADP.11: 16 residues within 4Å: Chain B: F.360 Chain L: D.205, I.206, G.207, G.208, P.247, G.248, T.249, G.250, T.252, L.253, D.304, I.380, H.384, G.408, A.409 7 PLIP interactions: 7 interactions with chain L Hydrogen bonds: L:G.207, L:G.208, L:G.248, L:T.249, L:T.252, L:L.253, L:D.304 ADP.12: 15 residues within 4Å: Chain L: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, N.660, G.684, A.685, T.688 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:G.480, L:G.521, L:C.522, L:G.523, L:K.524, L:T.525, L:T.525, L:T.525, L:L.526, L:T.688

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Braxton, J.R. et al., The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-06-21

Peptides

UBX domain-containing protein 6: ACEGIK
Transitional endoplasmic reticulum ATPase: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
K

E
J

G
I

I
H

K
G

B
F

D
E

F
D

H
C

J
B

L
A

UBX domain-containing protein 6

Transitional endoplasmic reticulum ATPase

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