SMTL ID : 9i62.1

CryoEM structure of a RAD51 D-loop

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.64 Å

Oligo State

homo-9-mer

Ligands

18 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 4 residues within 4Å: Chain A: T.134, E.163, D.222 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.134 CA.2: 1 residues within 4Å: Ligands: ATP.3 No protein-ligand interaction detected (PLIP) CA.4: 5 residues within 4Å: Chain A: A.293, H.294, S.296, D.316 Ligands: ATP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.293, A:S.296, A:D.316 CA.5: 4 residues within 4Å: Chain B: T.134, E.163, T.165 Ligands: ATP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.134, B:E.163 CA.7: 5 residues within 4Å: Chain B: A.293, H.294, S.296, D.316 Ligands: ATP.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.293, B:S.296, B:D.316 CA.8: 4 residues within 4Å: Chain C: T.134, E.163, T.165 Ligands: ATP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.134, C:E.163 CA.10: 5 residues within 4Å: Chain C: A.293, H.294, S.296, D.316 Ligands: ATP.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.293, C:S.296, C:D.316 CA.11: 4 residues within 4Å: Chain D: T.134, E.163, T.165 Ligands: ATP.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.134, D:E.163 CA.13: 5 residues within 4Å: Chain D: A.293, H.294, S.296, D.316 Ligands: ATP.15 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:A.293, D:S.296, D:D.316 CA.14: 4 residues within 4Å: Chain E: T.134, E.163, T.165 Ligands: ATP.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.134, E:E.163 CA.16: 5 residues within 4Å: Chain E: A.293, H.294, S.296, D.316 Ligands: ATP.18 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:A.293, E:S.296, E:D.316 CA.17: 4 residues within 4Å: Chain F: T.134, E.163, T.165 Ligands: ATP.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.134, F:E.163 CA.19: 5 residues within 4Å: Chain F: A.293, H.294, S.296, D.316 Ligands: ATP.21 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:A.293, F:S.296, F:D.316 CA.20: 4 residues within 4Å: Chain G: T.134, E.163, T.165 Ligands: ATP.21 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.134, G:E.163 CA.22: 5 residues within 4Å: Chain G: A.293, H.294, S.296, D.316 Ligands: ATP.24 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:A.293, G:S.296, G:D.316 CA.23: 4 residues within 4Å: Chain H: T.134, E.163, T.165 Ligands: ATP.24 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.134, H:E.163 CA.25: 6 residues within 4Å: Chain H: A.293, H.294, S.296, T.297, D.316 Ligands: ATP.27 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:S.296, H:D.316 CA.26: 5 residues within 4Å: Chain I: T.134, E.163, T.165, D.222 Ligands: ATP.27 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:T.134, I:E.163

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

ATP.3: 15 residues within 4Å: Chain A: E.128, F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, A.331 Ligands: CA.1, CA.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.130, A:R.130, A:T.131, A:G.132, A:K.133, A:T.134, A:T.134, A:Q.135, A:Q.135, A:E.163, A:R.170, A:R.170, A:R.310 Salt bridges: A:K.133, A:K.133 ATP.6: 24 residues within 4Å: Chain A: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain B: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.4, CA.5 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.130, B:R.130, B:T.131, B:G.132, B:K.133, B:T.134, B:T.134, B:Q.135, B:Q.135, B:R.310, A:C.319, A:E.322 Salt bridges: B:K.133, B:K.133, A:H.294 ATP.9: 25 residues within 4Å: Chain B: A.293, H.294, Y.315, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain C: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.7, CA.8 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:C.319, B:E.322, C:R.130, C:R.130, C:G.132, C:K.133, C:T.134, C:Q.135, C:Q.135, C:R.310 Salt bridges: B:H.294, C:K.133, C:K.133 ATP.12: 25 residues within 4Å: Chain C: A.293, H.294, Y.315, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain D: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.10, CA.11 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.130, D:R.130, D:T.131, D:G.132, D:G.132, D:K.133, D:T.134, D:Q.135, D:Q.135, D:R.310, C:C.319, C:E.322 Salt bridges: D:K.133, D:K.133, C:H.294 ATP.15: 24 residues within 4Å: Chain D: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain E: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.13, CA.14 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:R.130, E:R.130, E:T.131, E:G.132, E:K.133, E:T.134, E:Q.135, E:Q.135, E:R.310, D:C.319, D:E.322 Salt bridges: E:K.133, E:K.133, D:H.294 ATP.18: 24 residues within 4Å: Chain E: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain F: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.16, CA.17 15 PLIP interactions: 3 interactions with chain E, 12 interactions with chain F Hydrogen bonds: E:C.319, E:E.322, F:R.130, F:R.130, F:T.131, F:T.131, F:G.132, F:K.133, F:T.134, F:Q.135, F:Q.135, F:R.310 Salt bridges: E:H.294, F:K.133, F:K.133 ATP.21: 24 residues within 4Å: Chain F: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain G: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.19, CA.20 17 PLIP interactions: 14 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:R.130, G:R.130, G:T.131, G:T.131, G:G.132, G:K.133, G:T.134, G:T.134, G:Q.135, G:Q.135, G:R.170, G:R.310, F:C.319, F:E.322 Salt bridges: G:K.133, G:K.133, F:H.294 ATP.24: 26 residues within 4Å: Chain G: A.293, H.294, S.296, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain H: E.128, F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.22, CA.23 17 PLIP interactions: 14 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:R.130, H:R.130, H:T.131, H:T.131, H:G.132, H:K.133, H:T.134, H:T.134, H:Q.135, H:Q.135, H:R.170, H:R.310, G:C.319, G:E.322 Salt bridges: H:K.133, H:K.133, G:H.294 ATP.27: 23 residues within 4Å: Chain H: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain I: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, A.331 Ligands: CA.25, CA.26 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:R.130, I:R.130, I:T.131, I:G.132, I:K.133, I:T.134, I:T.134, I:Q.135, I:Q.135, I:R.170, I:R.310 Salt bridges: I:K.133, I:K.133, H:H.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joudeh, L. et al., Structural mechanism of strand exchange by the RAD51 filament. Elife (2025)

Release Date

2025-06-04

Peptides

DNA repair protein RAD51 homolog 1: ABCDEFGHI

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

DNA repair protein RAD51 homolog 1

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