SMTL ID : 6oa9.1

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

hetero-6-3-1-mer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: D.215, I.216, G.217, G.258, T.259, G.260, K.261, T.262, L.263, D.314, E.315, H.394, G.418, A.419, A.422 Chain B: F.370 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.215, A:G.217, A:G.258, A:T.259, A:G.260, A:K.261, A:T.262, A:T.262, A:T.262, A:L.263, A:D.314, A:E.315, A:E.315 Salt bridges: A:K.261, A:K.261 ATP.2: 16 residues within 4Å: Chain B: I.216, G.217, P.257, G.258, T.259, G.260, K.261, T.262, L.263, E.315, V.390, H.394, G.418, A.419, A.422 Chain C: R.369 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.217, B:G.217, B:G.258, B:T.259, B:G.260, B:K.261, B:T.262, B:T.262, B:T.262, B:L.263, B:E.315, C:R.369 Salt bridges: B:K.261, C:R.369, C:R.369 ATP.3: 16 residues within 4Å: Chain B: D.488, V.489, G.490, P.529, G.531, T.532, G.533, K.534, L.536, N.634, I.666, Q.670, G.694, L.698 Chain C: R.645, R.648 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.490, B:P.529, B:T.532, B:K.534, C:R.648 Salt bridges: B:K.534, C:R.645, C:R.645, C:R.645 ATP.4: 16 residues within 4Å: Chain C: I.216, G.217, G.258, T.259, G.260, K.261, T.262, L.263, D.314, H.394, V.417, G.418, A.419, A.422 Chain D: R.369, F.370 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.217, C:G.258, C:G.260, C:K.261, C:T.262, C:T.262, C:L.263, C:D.314, C:E.315 Salt bridges: C:K.261, C:K.261, D:R.369, D:R.369 ATP.5: 18 residues within 4Å: Chain C: D.488, V.489, G.490, P.530, G.531, T.532, G.533, K.534, T.535, L.536, Q.588, N.634, G.694, A.695, L.698 Chain D: L.615, R.645, R.648 14 PLIP interactions: 5 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:L.615, D:R.648, C:G.531, C:T.532, C:G.533, C:K.534, C:T.535, C:T.535, C:T.535, C:Q.588, C:N.634 Salt bridges: D:R.645, D:R.645, D:R.645 ATP.6: 18 residues within 4Å: Chain D: G.490, L.492, P.529, P.530, G.531, T.532, G.533, K.534, T.535, L.536, N.634, I.666, G.694, A.695, L.698 Chain E: D.619, R.645, R.648 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:P.529, D:G.531, D:T.532, D:G.533, D:K.534, D:T.535, D:L.536, E:R.645 Salt bridges: D:K.534, D:K.534, E:R.645, E:R.645, E:R.645 ATP.7: 17 residues within 4Å: Chain D: D.215, I.216, G.217, P.257, G.258, T.259, G.260, K.261, T.262, L.263, D.314, E.315, V.390, H.394, G.418, A.419 Chain E: R.369 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.217, D:G.258, D:G.260, D:K.261, D:T.262, D:T.262, D:L.263, D:E.315, D:E.315 pi-Stacking: D:H.394 Salt bridges: E:R.369, E:R.369 ATP.9: 14 residues within 4Å: Chain E: D.215, I.216, G.217, G.258, T.259, G.260, K.261, T.262, D.314, H.394, G.418, A.419, A.422 Chain F: R.369 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:I.216, E:G.258, E:G.260, E:K.261, E:T.262, E:L.263, E:D.314 Salt bridges: E:K.261, E:K.261, F:R.369, F:R.369 ATP.10: 13 residues within 4Å: Chain A: R.369 Chain F: I.216, G.217, P.257, G.258, T.259, G.260, K.261, T.262, L.263, H.394, G.418, A.419 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.217, F:G.258, F:T.259, F:G.260, F:K.261, F:T.262, F:T.262, F:G.418 Salt bridges: A:R.369

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.8: 14 residues within 4Å: Chain E: V.489, G.490, P.529, P.530, G.531, T.532, G.533, K.534, T.535, L.536, I.666, G.694, A.695, L.698 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.490, E:T.535, E:T.535, E:L.536 Salt bridges: E:K.534

2 x ZN: ZINC ION(Non-covalent)

ZN.11: 7 residues within 4Å: Chain J: C.137, H.139, M.144, C.145, E.146, Y.147, C.148 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:H.139, J:C.145 ZN.12: 5 residues within 4Å: Chain J: C.204, H.208, C.216, K.218, C.219 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:H.208, J:C.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Twomey, E.C. et al., Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Science (2019)

Release Date

2019-07-03

Peptides

Cell division control protein 48: ABCDEF
Ubiquitin: GHI
Nuclear protein localization protein 4: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
K

H
H

I
J

J
G

Cell division control protein 48

Ubiquitin

Nuclear protein localization protein 4

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