SMTL ID : 9njk.1

The Cryo-EM structure of the yeast Rad51-ssDNA nucleoprotein filament ADP bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.37 Å

Oligo State

homo-hexamer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.1: 17 residues within 4Å: Chain A: F.187, R.188, T.189, G.190, K.191, S.192, Q.193, R.228, Q.326, R.368, I.387, Y.388, E.389 Chain C: C.377, L.378, P.379 Ligands: MG.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.188, A:R.188, A:R.188, A:T.189, A:G.190, A:K.191, A:S.192, A:Q.193, A:Q.326, A:R.368, C:C.377 Salt bridges: A:K.191 ADP.3: 15 residues within 4Å: Chain A: L.378, E.380 Chain B: F.187, R.188, T.189, G.190, K.191, S.192, Q.193, R.228, Q.326, R.368, I.387, Y.388 Ligands: MG.4 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.188, B:R.188, B:R.188, B:T.189, B:G.190, B:S.192, B:S.192, B:Q.193, B:Q.193, B:R.228, B:Q.326, B:R.368, A:E.380, A:E.380 Salt bridges: B:K.191 ADP.5: 14 residues within 4Å: Chain B: S.375, P.376, E.380 Chain E: F.187, R.188, T.189, G.190, K.191, S.192, Q.193, R.228, I.387, E.389 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:R.188, E:T.189, E:T.189, E:G.190, E:K.191, E:S.192, E:Q.193, E:Q.193, E:R.228 Salt bridges: E:K.191 ADP.7: 14 residues within 4Å: Chain E: P.376, C.377, P.379 Chain F: E.186, F.187, R.188, T.189, G.190, K.191, S.192, Q.193, R.368, E.389 Ligands: MG.8 11 PLIP interactions: 1 interactions with chain E, 10 interactions with chain F Hydrogen bonds: E:C.377, F:R.188, F:T.189, F:G.190, F:K.191, F:S.192, F:S.192, F:Q.193, F:Q.193, F:R.368 Salt bridges: F:K.191

4 x MG: MAGNESIUM ION

MG.2: 3 residues within 4Å: Chain A: S.192, Q.326 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: S.192, T.223, D.280 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.192 MG.6: 3 residues within 4Å: Chain E: S.192, E.221 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.192 MG.8: 2 residues within 4Å: Chain F: S.192 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, Y. et al., ATP hydrolysis-driven structural transitions within the Saccharomyces cerevisiae Rad51 and Dmc1 nucleoprotein filaments. J.Biol.Chem. (2025)

Release Date

2025-03-19

Peptides

DNA repair protein RAD51: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
E

D
F

E
B

F
A

DNA repair protein RAD51

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