SMTL ID : 9e6l.1

Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to Rad54peptide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-5-6-mer

Ligands

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

ATP.1: 22 residues within 4Å: Chain G: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, R.149, R.289, I.308, E.310 Chain L: H.273, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Ligands: MG.3, MG.17 14 PLIP interactions: 2 interactions with chain L, 12 interactions with chain G Hydrogen bonds: L:H.273, L:C.298, G:R.109, 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: G:K.112, G:K.112 ATP.4: 13 residues within 4Å: Chain H: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289 Ligands: MG.6, MG.7 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:R.109, H:T.110, H:G.111, H:K.112, H:S.113, H:S.113, H:S.113, H:Q.114, H:R.289 Salt bridges: H:K.112, H:K.112 ATP.8: 22 residues within 4Å: Chain G: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300 Chain I: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289, E.310 Ligands: MG.2, MG.10 17 PLIP interactions: 12 interactions with chain I, 5 interactions with chain G Hydrogen bonds: I:E.107, I:R.109, I:T.110, I:G.111, I:K.112, I:S.113, I:S.113, I:Q.114, I:Q.114, I:R.289, G:H.273, G:D.295, G:S.296, G:C.298, G:E.301 Salt bridges: I:K.112, I:K.112 ATP.11: 21 residues within 4Å: Chain H: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300 Chain J: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289 Ligands: MG.5, MG.13 17 PLIP interactions: 12 interactions with chain J, 5 interactions with chain H Hydrogen bonds: J:E.107, J:R.109, J:T.110, J:G.111, J:K.112, J:S.113, J:S.113, J:Q.114, J:Q.114, J:R.289, H:H.273, H:D.295, H:S.296, H:C.298, H:E.301 Salt bridges: J:K.112, J:K.112 ATP.14: 22 residues within 4Å: Chain I: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300 Chain K: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289, E.310 Ligands: MG.9, MG.15 14 PLIP interactions: 4 interactions with chain I, 10 interactions with chain K Hydrogen bonds: I:D.295, I:S.296, I:C.298, K:T.110, K:G.111, K:K.112, K:S.113, K:S.113, K:Q.114, K:Q.114, K:R.289 Salt bridges: I:H.273, K:K.112, K:K.112 ATP.16: 21 residues within 4Å: Chain J: H.273, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Chain L: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, R.149, R.289, E.310 Ligands: MG.12, MG.18 15 PLIP interactions: 14 interactions with chain L, 1 interactions with chain J Hydrogen bonds: L:E.107, L:R.109, L:R.109, L:T.110, L:G.111, L:K.112, L:S.113, L:S.113, L:Q.114, L:Q.114, L:R.149, L:R.289, J:H.273 Salt bridges: L:K.112, L:K.112

12 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain G: S.275, T.276, D.295 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.295 MG.3: 3 residues within 4Å: Chain G: S.113, T.144 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.113 MG.5: 4 residues within 4Å: Chain H: S.275, T.276, D.295 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.295 MG.6: 2 residues within 4Å: Chain H: S.113 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.113 MG.7: 1 residues within 4Å: Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain I: S.275, T.276, D.295 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.295 MG.10: 2 residues within 4Å: Chain I: S.113 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.113 MG.12: 3 residues within 4Å: Chain J: S.275, D.295 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.295 MG.13: 2 residues within 4Å: Chain J: S.113 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.113 MG.15: 2 residues within 4Å: Chain K: S.113 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.113 MG.17: 4 residues within 4Å: Chain L: S.275, T.276, D.295 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.295 MG.18: 2 residues within 4Å: Chain L: S.113 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:S.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, Y. et al., Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to Rad54peptide. To Be Published

Release Date

2025-01-22

Peptides

DNA repair and recombination protein RAD54: ABCDE
DNA repair protein RAD51: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

G
C

H
F

I
B

J
E

K
A

L
D

DNA repair and recombination protein RAD54

DNA repair protein RAD51

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