SMTL ID : 8daw.1

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uD)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-1-4-mer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: I.219, G.220, P.260, G.261, T.262, G.263, K.264, T.265, L.266, D.317, E.318, V.393, H.397, G.421 Chain B: F.373 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.220, A:G.220, A:G.261, A:T.262, A:G.263, A:K.264, A:T.265, A:T.265, A:T.265, A:D.317, A:E.318 Salt bridges: A:K.264, A:K.264 ATP.3: 17 residues within 4Å: Chain B: D.218, I.219, G.220, P.260, G.261, T.262, G.263, K.264, T.265, L.266, D.317, V.393, H.397, G.421, A.422 Chain C: D.346, F.373 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.220, B:G.220, B:G.261, B:G.263, B:K.264, B:T.265, B:T.265, B:L.266, B:D.317, C:R.375 Salt bridges: B:K.264, B:K.264 ATP.5: 18 residues within 4Å: Chain C: D.218, I.219, G.220, P.260, G.261, T.262, G.263, K.264, T.265, L.266, D.317, E.318, H.397, G.421, A.422 Chain D: R.372, F.373, R.375 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.220, C:G.220, C:G.261, C:T.262, C:G.263, C:K.264, C:T.265, C:T.265, C:E.318, C:E.318, D:R.372, D:R.375 Salt bridges: C:K.264, C:K.264 ATP.7: 16 residues within 4Å: Chain D: D.218, I.219, G.220, P.260, G.261, T.262, G.263, K.264, T.265, L.266, D.317, H.397, G.421, A.422 Chain E: R.372, F.373 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.220, D:G.220, D:G.261, D:T.262, D:G.263, D:K.264, D:T.265, D:T.265, D:T.265, D:D.317 Salt bridges: D:K.264, D:K.264 ATP.11: 14 residues within 4Å: Chain A: R.372 Chain F: D.218, I.219, G.220, G.261, T.262, G.263, K.264, T.265, L.266, D.317, H.397, G.421, A.422 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.220, F:G.220, F:G.261, F:G.263, F:K.264, F:T.265, F:T.265, F:T.265, F:L.266, F:D.317 Salt bridges: F:K.264, F:K.264, A:R.372

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

ADP.2: 14 residues within 4Å: Chain A: D.491, V.492, G.493, P.533, G.534, T.535, G.536, K.537, T.538, L.539, I.669, Q.673, G.697, L.701 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.493, A:G.534, A:T.535, A:G.536, A:K.537, A:T.538, A:T.538, A:L.539 Salt bridges: A:K.537 ADP.4: 14 residues within 4Å: Chain B: V.492, G.493, G.494, G.534, T.535, G.536, K.537, T.538, L.539, P.661, I.669, Q.673, G.697, L.701 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.493, B:G.494, B:G.534, B:T.535, B:G.536, B:K.537, B:T.538, B:T.538, B:T.538, B:Q.673, B:G.697 ADP.6: 12 residues within 4Å: Chain C: G.493, P.533, G.534, T.535, G.536, K.537, T.538, L.539, D.590, I.669, G.697, A.698 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.493, C:G.493, C:G.534, C:G.536, C:K.537, C:T.538, C:T.538, C:T.538, C:D.590, C:G.697 Salt bridges: C:K.537 ADP.8: 10 residues within 4Å: Chain D: G.493, P.533, G.534, T.535, G.536, K.537, T.538, L.539, I.669, G.697 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.493, D:G.534, D:G.536, D:K.537, D:T.538, D:T.538, D:T.538 Salt bridges: D:K.537, D:K.537 ADP.9: 14 residues within 4Å: Chain E: D.218, I.219, G.220, G.261, T.262, G.263, K.264, T.265, L.266, H.397, G.421, A.422 Chain F: R.372, F.373 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.220, E:G.220, E:G.261, E:T.262, E:G.263, E:K.264, E:T.265, E:T.265, E:L.266 Salt bridges: E:K.264, F:R.372 ADP.10: 13 residues within 4Å: Chain E: D.491, V.492, G.493, G.534, T.535, G.536, K.537, T.538, L.539, I.669, G.697, A.698, L.701 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.493, E:G.534, E:T.535, E:G.536, E:K.537, E:T.538, E:T.538, E:T.538, E:L.539, E:G.697 Salt bridges: E:K.537 ADP.12: 11 residues within 4Å: Chain F: V.492, G.493, G.534, T.535, G.536, K.537, T.538, L.539, I.669, Q.673, L.701 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.493, F:G.493, F:G.534, F:T.535, F:G.536, F:K.537, F:T.538 Salt bridges: F:K.537

2 x ZN: ZINC ION(Non-covalent)

ZN.13: 4 residues within 4Å: Chain G: C.140, H.142, C.148, C.151 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.140, G:H.142, G:C.148, G:C.151 ZN.14: 4 residues within 4Å: Chain G: C.207, H.211, C.219, C.222 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.207, G:H.211, G:C.219, G:C.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, H.G. et al., SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2022-11-30

Peptides

Cell division control protein 48: ABCDEF
Nuclear protein localization protein 4: G
Ubiquitin fusion degradation protein 1: H
Ubiquitin: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Cell division control protein 48

Nuclear protein localization protein 4

Ubiquitin fusion degradation protein 1

Ubiquitin

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