SMTL ID : 9e6n.1

Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to Hed1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.80 Å

Oligo State

hetero-6-5-mer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289, E.310 Chain B: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Ligands: MG.2 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:E.107, A:R.109, A:T.110, A:G.111, A:K.112, A:S.113, A:Q.114, A:Q.114, A:R.289, B:D.295, B:S.296, B:C.298, B:E.301, B:E.301 Salt bridges: A:K.112, A:K.112, B:H.273 ATP.3: 21 residues within 4Å: Chain B: F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289, E.310 Chain C: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Ligands: MG.4 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:R.109, B:T.110, B:T.110, B:G.111, B:K.112, B:S.113, B:Q.114, B:Q.114, B:R.149, B:R.289, C:D.295, C:S.296, C:E.301, C:E.301 Salt bridges: B:K.112, B:K.112, C:H.273 ATP.5: 21 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, E.310 Chain D: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300 Ligands: MG.6 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:R.109, C:T.110, C:T.110, C:G.111, C:K.112, C:S.113, C:S.113, C:Q.114, C:Q.114, C:R.289, D:D.295, D:S.296, D:C.298 Salt bridges: C:K.112, C:K.112, D:H.273 ATP.7: 21 residues within 4Å: Chain D: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, E.142, R.149, R.289 Chain E: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Ligands: MG.8 16 PLIP interactions: 10 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:R.109, D:T.110, D:G.111, D:K.112, D:S.113, D:Q.114, D:Q.114, D:R.289, E:D.295, E:S.296, E:C.298, E:E.301, E:E.301 Salt bridges: D:K.112, D:K.112, E:H.273 ATP.9: 24 residues within 4Å: 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 Chain F: H.273, V.294, D.295, S.296, P.297, C.298, L.299, P.300, E.301 Ligands: MG.10 18 PLIP interactions: 12 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:R.109, 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, F:D.295, F:S.296, F:C.298, F:E.301, F:E.301 Salt bridges: E:K.112, E:K.112, F:H.273 ATP.11: 11 residues within 4Å: Chain F: E.107, F.108, R.109, T.110, G.111, K.112, S.113, Q.114, R.149, R.289 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:R.109, F:R.109, F:T.110, F:G.111, F:K.112, F:S.113, F:S.113, F:S.113, F:Q.114, F:Q.114, F:R.149, F:R.289 Salt bridges: F:K.112, F:K.112 pi-Cation interactions: F:R.149

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.113 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.113 MG.4: 3 residues within 4Å: Chain B: S.113, D.201 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.113 MG.6: 2 residues within 4Å: Chain C: S.113 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.113 MG.8: 4 residues within 4Å: Chain D: S.113, E.142, D.201 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.113 MG.10: 3 residues within 4Å: Chain E: S.113, D.201 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.113 MG.12: 2 residues within 4Å: Chain F: S.113 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F: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 Hed1. To Be Published

Release Date

2025-01-22

Peptides

DNA repair protein RAD51: ABCDEF
Meiosis-specific protein HED1: GHIJK

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

J
J

K
K

DNA repair protein RAD51

Meiosis-specific protein HED1

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