SMTL ID : 8bsc.1

CryoEM structure of the RAD51 nucleoprotein filament in the presence of ADP and Ca2+

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

7 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: T.134, E.163, T.165 Ligands: ADP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.134, A:E.163, A:E.163 CA.3: 4 residues within 4Å: Chain B: T.134, E.163, T.165 Ligands: ADP.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.134, B:E.163, B:E.163 CA.5: 4 residues within 4Å: Chain C: T.134, E.163, T.165 Ligands: ADP.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.134, C:E.163, C:E.163 CA.7: 4 residues within 4Å: Chain D: T.134, E.163, T.165 Ligands: ADP.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.134, D:E.163, D:E.163 CA.9: 4 residues within 4Å: Chain E: T.134, E.163, T.165 Ligands: ADP.10 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.134, E:E.163, E:E.163 CA.11: 4 residues within 4Å: Chain F: T.134, E.163, T.165 Ligands: ADP.12 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.134, F:E.163, F:E.163 CA.13: 4 residues within 4Å: Chain G: T.134, E.163, T.165 Ligands: ADP.14 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.134, G:E.163, G:E.163

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

ADP.2: 16 residues within 4Å: Chain A: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, K.304, R.310, I.329, N.330, A.331 Chain D: P.318, E.322 Ligands: CA.1 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.130, A:T.131, A:G.132, A:K.133, A:T.134, A:T.134, A:Q.135, A:K.304, A:K.304, A:R.310, D:P.318, D:E.322 Salt bridges: A:K.133 ADP.4: 14 residues within 4Å: Chain B: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, K.304, R.310, I.329, N.330, A.331 Ligands: CA.3 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.130, B:T.131, B:G.132, B:K.133, B:T.134, B:T.134, B:Q.135, B:K.304, B:K.304, B:R.310 Salt bridges: B:K.133 ADP.6: 16 residues within 4Å: Chain B: P.318, E.322 Chain C: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, K.304, R.310, I.329, N.330, A.331 Ligands: CA.5 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:P.318, B:E.322, C:R.130, C:T.131, C:G.132, C:K.133, C:T.134, C:T.134, C:Q.135, C:K.304, C:K.304, C:R.310 Salt bridges: C:K.133 ADP.8: 16 residues within 4Å: Chain C: P.318, E.322 Chain D: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, K.304, R.310, I.329, N.330, A.331 Ligands: CA.7 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.130, D:T.131, D:G.132, D:K.133, D:T.134, D:T.134, D:Q.135, D:K.304, D:K.304, D:R.310, C:P.318, C:E.322 Salt bridges: D:K.133 ADP.10: 16 residues within 4Å: Chain A: P.318, E.322 Chain E: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, K.304, R.310, I.329, N.330, A.331 Ligands: CA.9 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:R.130, E:T.131, E:G.132, E:K.133, E:T.134, E:T.134, E:Q.135, E:K.304, E:K.304, E:R.310, A:P.318, A:E.322 Salt bridges: E:K.133 ADP.12: 16 residues within 4Å: Chain E: P.318, E.322 Chain F: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, K.304, R.310, I.329, N.330, A.331 Ligands: CA.11 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:R.130, F:T.131, F:G.132, F:K.133, F:T.134, F:T.134, F:Q.135, F:K.304, F:K.304, F:R.310, E:P.318, E:E.322 Salt bridges: F:K.133 ADP.14: 16 residues within 4Å: Chain F: P.318, E.322 Chain G: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, K.304, R.310, I.329, N.330, A.331 Ligands: CA.13 13 PLIP interactions: 11 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:R.130, G:T.131, G:G.132, G:K.133, G:T.134, G:T.134, G:Q.135, G:K.304, G:K.304, G:R.310, F:P.318, F:E.322 Salt bridges: G:K.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Appleby, R. et al., A metal ion-dependent mechanism of RAD51 nucleoprotein filament disassembly. Iscience (2023)

Release Date

2023-05-03

Peptides

DNA repair protein RAD51 homolog 1: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

E
E

F
F

G
G

DNA repair protein RAD51 homolog 1

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