SMTL ID : 8fcl.1

Cryo-EM structure of p97:UBXD1 closed state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, I.380, H.384, G.408, A.409 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.207, A:G.248, A:T.249, A:T.252, A:T.252 ADP.2: 15 residues within 4Å: Chain A: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, G.684, A.685, T.688 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.480, A:G.480, A:G.521, A:G.523, A:K.524, A:T.525, A:T.525, A:T.525, A:N.624 ADP.3: 13 residues within 4Å: Chain B: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, D.304, I.380, H.384, G.408, A.409 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.207, B:G.248, B:T.249, B:T.252 ADP.4: 14 residues within 4Å: Chain B: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.480, B:G.480, B:G.521, B:G.523, B:K.524, B:T.525, B:T.525, B:T.525, B:L.526 ADP.5: 15 residues within 4Å: Chain B: R.359, F.360 Chain C: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain C Salt bridges: B:R.359 Hydrogen bonds: C:G.207, C:G.248, C:T.249, C:G.250, C:K.251, C:T.252, C:T.252 ADP.6: 14 residues within 4Å: Chain C: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, G.684, A.685, T.688 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.480, C:G.480, C:G.523, C:K.524, C:T.525, C:T.525, C:T.525, C:L.526, C:D.577, C:D.577 ADP.7: 16 residues within 4Å: Chain C: R.359, F.360 Chain D: 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 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.207, D:G.208, D:G.248, D:T.249, D:G.250, D:K.251, D:T.252, D:T.252 Salt bridges: C:R.359 ADP.8: 15 residues within 4Å: Chain C: R.635 Chain D: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.480, D:G.480, D:G.521, D:G.523, D:K.524, D:T.525, D:T.525, D:T.525, D:L.526, C:R.635 ADP.9: 16 residues within 4Å: Chain D: R.359, F.360 Chain E: 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 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.207, E:G.248, E:T.249, E:G.250, E:K.251, E:T.252, E:T.252, E:T.252 Salt bridges: D:R.359 ADP.10: 13 residues within 4Å: Chain E: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, G.684, A.685, T.688 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.480, E:G.480, E:G.521, E:G.523, E:T.525, E:T.525, E:T.525, E:L.526, E:D.577 ADP.11: 16 residues within 4Å: Chain E: R.359, F.360 Chain F: 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 8 PLIP interactions: 1 interactions with chain E, 7 interactions with chain F Salt bridges: E:R.359 Hydrogen bonds: F:G.207, F:G.208, F:G.248, F:G.250, F:K.251, F:T.252, F:T.252 ADP.12: 14 residues within 4Å: Chain F: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 8 PLIP interactions: 8 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:L.526

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

Transitional endoplasmic reticulum ATPase: ABCDEF
UBX domain-containing protein 6: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Transitional endoplasmic reticulum ATPase

UBX domain-containing protein 6

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