SMTL ID : 8bq2.1

CryoEM structure of the pre-synaptic RAD51 nucleoprotein filament in the presence of ATP and Ca2+

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-9-mer

Ligands

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

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

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

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

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: 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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