SMTL ID : 7pbm.1

RuvAB branch migration motor complexed to the Holliday junction - RuvB AAA+ state s2 [t2 dataset]

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-1-mer

Ligands

3 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 22 residues within 4Å: Chain A: L.2, R.3, P.4, Y.10, I.11, P.43, G.44, L.45, G.46, K.47, T.48, T.49, T.141, Y.163, I.171, R.174, P.199, R.200, N.203 Chain F: E.110, R.153 Ligands: MG.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:I.11, A:G.44, A:L.45, A:G.46, A:K.47, A:T.48, A:T.49, A:T.49, A:Y.163, A:R.200, A:N.203, F:R.153 Salt bridges: A:R.3, A:K.47, A:R.200, A:R.200 AGS.3: 24 residues within 4Å: Chain A: E.110, P.149, R.153 Chain B: L.2, R.3, P.4, Y.10, I.11, P.43, G.44, L.45, G.46, K.47, T.48, T.49, E.93, T.141, Y.163, I.171, R.174, P.199, R.200, N.203 Ligands: MG.4 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.2, B:I.11, B:G.44, B:L.45, B:G.46, B:K.47, B:T.48, B:T.49, B:T.49, B:Y.163, B:Y.163, B:R.200, B:N.203, A:R.153, A:R.153 Salt bridges: B:R.3, B:K.47, B:R.200, B:R.200 AGS.5: 23 residues within 4Å: Chain B: E.110, P.149, R.153 Chain C: L.2, R.3, P.4, Y.10, I.11, P.43, G.44, L.45, G.46, K.47, T.48, T.49, T.141, Y.163, I.171, R.174, P.199, R.200, N.203 Ligands: MG.6 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:L.2, C:L.2, C:I.11, C:G.44, C:L.45, C:G.46, C:K.47, C:T.48, C:T.49, C:T.49, C:Y.163, C:Y.163, C:R.200, C:R.200, B:R.153, B:R.153 Salt bridges: C:R.3, C:K.47, C:R.200, C:R.200

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.48, D.92 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.48 MG.4: 4 residues within 4Å: Chain A: R.153 Chain B: T.48, D.92 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.48 MG.6: 4 residues within 4Å: Chain B: R.153 Chain C: T.48, D.92 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.48

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

ADP.7: 15 residues within 4Å: Chain D: T.1, L.2, P.4, Y.10, I.11, G.44, L.45, G.46, K.47, T.48, T.49, Y.163, I.171, P.199, R.200 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:L.2, D:Y.10, D:G.44, D:G.46, D:K.47, D:T.48, D:T.48, D:Y.163 ADP.8: 17 residues within 4Å: Chain E: L.2, R.3, P.4, Y.10, I.11, G.44, L.45, G.46, K.47, T.48, T.49, Y.163, I.171, R.174, P.199, R.200, N.203 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:I.11, E:G.44, E:L.45, E:G.46, E:G.46, E:K.47, E:T.48, E:T.48, E:T.49, E:T.49, E:Y.163, E:Y.163, E:R.174 Salt bridges: E:R.200 ADP.9: 18 residues within 4Å: Chain F: L.2, R.3, P.4, Y.10, I.11, P.43, G.44, L.45, G.46, K.47, T.48, T.49, Y.163, I.171, R.174, P.199, R.200, N.203 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:I.11, F:G.44, F:L.45, F:G.46, F:K.47, F:T.48, F:T.48, F:T.49, F:T.49, F:Y.163, F:N.203 Salt bridges: F:K.47, F:R.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wald, J. et al., Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration. Nature (2022)

Release Date

2022-09-14

Peptides

Holliday junction ATP-dependent DNA helicase RuvB: ABCDEF
Holliday junction ATP-dependent DNA helicase RuvA: G
Holliday junction ATP-dependent DNA helicase RuvA: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Holliday junction ATP-dependent DNA helicase RuvB

Holliday junction ATP-dependent DNA helicase RuvA

Holliday junction ATP-dependent DNA helicase RuvA

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