SMTL ID : 8br2.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

CA.1: 4 residues within 4Å: Chain A: T.134, E.163, T.165 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.134, A:E.163 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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:A.293, A:H.294, 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 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:A.293, B:H.294, 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 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:A.293, C:H.294, 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 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:A.293, D:H.294, 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 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:A.293, E:H.294, 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

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

ATP.3: 16 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, N.330, A.331 Ligands: CA.1, CA.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.130, A:R.130, A:T.131, A:T.131, A:G.132, A:K.133, A:T.134, A:Q.135, A:Q.135, A:R.170 Salt bridges: A:K.133, A:K.133 ATP.6: 25 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, I.329, N.330, A.331 Ligands: CA.4, CA.5 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.130, B:R.130, B:T.131, B:T.131, B:G.132, B:K.133, B:T.134, B:Q.135, B:Q.135, 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, 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, I.329, N.330, A.331 Ligands: CA.7, CA.8 12 PLIP interactions: 10 interactions with chain C, 2 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:Q.135, C:Q.135, B:C.319 Salt bridges: C:K.133, C:K.133, B:H.294 ATP.12: 25 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, I.329, N.330, A.331 Ligands: CA.10, CA.11 12 PLIP interactions: 10 interactions with chain D, 2 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:Q.135, D:Q.135, C:C.319 Salt bridges: D:K.133, D:K.133, C:H.294 ATP.15: 25 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, I.329, N.330, A.331 Ligands: CA.13, CA.14 13 PLIP interactions: 3 interactions with chain D, 10 interactions with chain E Hydrogen bonds: D:C.319, D:E.322, E:R.130, E:R.130, E:T.131, E:G.132, E:K.133, E:T.134, E:Q.135, E:Q.135 Salt bridges: D:H.294, E:K.133, E:K.133 ATP.18: 25 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, I.329, N.330, A.331 Ligands: CA.16, CA.17 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain E Hydrogen bonds: 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, E:C.319 Salt bridges: F:K.133, F:K.133, E:H.294

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DNA repair protein RAD51 homolog 1

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