SMTL ID : 9d46.1

The cryo-EM structure of the yeast RAD51 filament bound to ssDNA in the presence of ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.06 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 25 residues within 4Å: Chain B: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289, I.308, Y.309, E.310 Chain G: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Ligands: MG.3, MG.17 17 PLIP interactions: 5 interactions with chain G, 12 interactions with chain B Hydrogen bonds: G:S.296, G:C.298, G:E.301, G:E.301, B:R.109, B:T.110, B:G.111, B:K.112, B:S.113, B:S.113, B:Q.114, B:Q.114, B:E.142, B:R.289 Salt bridges: G:H.273, B:K.112, B:K.112 ATP.4: 16 residues within 4Å: Chain C: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289, I.308, Y.309, E.310 Ligands: MG.6, MG.7 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:R.109, C:R.109, C:T.110, C:G.111, C:K.112, C:S.113, C:S.113, C:Q.114, C:R.149, C:R.289 Salt bridges: C:K.112, C:K.112 ATP.8: 25 residues within 4Å: Chain B: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Chain D: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289, I.308, Y.309, E.310 Ligands: MG.2, MG.10 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:E.107, D:R.109, D:T.110, D:T.110, D:G.111, D:K.112, D:S.113, D:S.113, D:Q.114, D:Q.114, D:E.142, D:R.289, B:S.296, B:C.298, B:E.301, B:E.301 Salt bridges: D:K.112, D:K.112, B:H.273 ATP.11: 25 residues within 4Å: Chain C: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Chain E: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289, I.308, Y.309, E.310 Ligands: MG.5, MG.13 18 PLIP interactions: 13 interactions with chain E, 5 interactions with chain C Hydrogen bonds: E:R.109, E:T.110, E:T.110, E:T.110, E:G.111, E:K.112, E:S.113, E:S.113, E:Q.114, E:Q.114, E:R.289, C:S.296, C:C.298, C:E.301, C:E.301 Salt bridges: E:K.112, E:K.112, C:H.273 ATP.14: 25 residues within 4Å: Chain D: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Chain F: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289, I.308, Y.309, E.310 Ligands: MG.9, MG.15 20 PLIP interactions: 15 interactions with chain F, 5 interactions with chain D Hydrogen bonds: F:E.107, F:R.109, F:T.110, F:T.110, F:G.111, F:K.112, F:S.113, F:S.113, F:Q.114, F:Q.114, F:E.142, F:R.149, F:R.289, D:S.296, D:C.298, D:E.301, D:E.301 Salt bridges: F:K.112, F:K.112, D:H.273 ATP.16: 26 residues within 4Å: Chain E: A.272, H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Chain G: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289, I.308, Y.309, E.310 Ligands: MG.12, MG.18 18 PLIP interactions: 6 interactions with chain E, 12 interactions with chain G Hydrogen bonds: E:A.272, E:S.296, E:C.298, E:E.301, E:E.301, G:E.107, G:R.109, G:T.110, G:G.111, G:K.112, G:S.113, G:S.113, G:Q.114, G:Q.114, G:R.289 Salt bridges: E:H.273, G:K.112, G:K.112

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: S.275, T.276, D.295 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.295, B:D.295 MG.3: 3 residues within 4Å: Chain B: S.113, D.201 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.113 MG.5: 4 residues within 4Å: Chain C: S.275, T.276, D.295 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.295, C:D.295 MG.6: 5 residues within 4Å: Chain C: S.113, E.142, T.144, D.201 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.113, C:D.201, C:D.201 MG.7: 2 residues within 4Å: Chain C: R.109 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain D: S.275, T.276, D.295 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.295, D:D.295 MG.10: 2 residues within 4Å: Chain D: S.113 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.113 MG.12: 4 residues within 4Å: Chain E: S.275, T.276, D.295 Ligands: ATP.16 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.295, E:D.295 MG.13: 2 residues within 4Å: Chain E: S.113 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.113 MG.15: 5 residues within 4Å: Chain F: S.113, E.142, T.144, D.201 Ligands: ATP.14 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:S.113, F:D.201, F:D.201 MG.17: 4 residues within 4Å: Chain G: S.275, T.276, D.295 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.295, G:D.295 MG.18: 3 residues within 4Å: Chain G: S.113, D.201 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, Y. et al., The cryo-EM structure of the yeast RAD51 filament bound to ssDNA in the presence of ATP. To Be Published

Release Date

2025-02-19

Peptides

DNA repair protein RAD51: BCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
C

C
F

D
B

E
E

F
A

G
D

DNA repair protein RAD51

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