SMTL ID : 5np7.1

CryoEM structure of Human Rad51 on single-stranded DNA to 4.2A resolution.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.20 Å

Oligo State

homo-heptamer

Ligands

7 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 22 residues within 4Å: Chain A: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, R.310, I.329, N.330, A.331 Chain B: H.294, S.296, Y.315, D.316, S.317, P.318, C.319, L.320, P.321, E.322 18 PLIP interactions: 7 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:H.294, B:H.294, B:Y.315, B:D.316, B:S.317, B:C.319, B:E.322, A:R.130, A:R.130, A:G.132, A:K.133, A:K.133, A:K.133, A:T.134, A:T.134, A:T.134, A:Q.135, A:R.310 ANP.2: 22 residues within 4Å: Chain B: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, R.310, I.329, N.330, A.331 Chain C: H.294, S.296, Y.315, D.316, S.317, P.318, C.319, L.320, P.321, E.322 19 PLIP interactions: 7 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:H.294, C:H.294, C:Y.315, C:D.316, C:S.317, C:C.319, C:E.322, B:R.130, B:R.130, B:R.130, B:G.132, B:K.133, B:K.133, B:K.133, B:T.134, B:T.134, B:T.134, B:Q.135, B:R.310 ANP.3: 22 residues within 4Å: Chain C: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, R.310, I.329, N.330, A.331 Chain D: H.294, S.296, Y.315, D.316, S.317, P.318, C.319, L.320, P.321, E.322 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:R.130, C:R.130, C:G.132, C:K.133, C:K.133, C:K.133, C:T.134, C:T.134, C:T.134, C:Q.135, C:R.310, D:H.294, D:H.294, D:Y.315, D:D.316, D:S.317, D:C.319, D:E.322 ANP.4: 22 residues within 4Å: Chain D: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, R.310, I.329, N.330, A.331 Chain E: H.294, S.296, Y.315, D.316, S.317, P.318, C.319, L.320, P.321, E.322 18 PLIP interactions: 7 interactions with chain E, 11 interactions with chain D Hydrogen bonds: E:H.294, E:H.294, E:Y.315, E:D.316, E:S.317, E:C.319, E:E.322, D:R.130, D:R.130, D:G.132, D:K.133, D:K.133, D:K.133, D:T.134, D:T.134, D:T.134, D:Q.135, D:R.310 ANP.5: 21 residues within 4Å: Chain E: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, R.310, I.329, N.330, A.331 Chain F: H.294, S.296, Y.315, D.316, S.317, P.318, C.319, L.320, P.321 18 PLIP interactions: 11 interactions with chain E, 7 interactions with chain F Hydrogen bonds: E:R.130, E:R.130, E:G.132, E:K.133, E:K.133, E:K.133, E:T.134, E:T.134, E:T.134, E:Q.135, E:R.310, F:H.294, F:H.294, F:Y.315, F:D.316, F:S.317, F:C.319, F:E.322 ANP.6: 22 residues within 4Å: Chain F: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, R.310, I.329, N.330, A.331 Chain G: H.294, S.296, Y.315, D.316, S.317, P.318, C.319, L.320, P.321, E.322 18 PLIP interactions: 7 interactions with chain G, 11 interactions with chain F Hydrogen bonds: G:H.294, G:S.296, G:Y.315, G:D.316, G:S.317, G:C.319, G:E.322, F:R.130, F:R.130, F:G.132, F:K.133, F:K.133, F:K.133, F:T.134, F:T.134, F:T.134, F:Q.135, F:R.310 ANP.7: 9 residues within 4Å: Chain G: R.130, T.131, G.132, K.133, T.134, Q.135, R.170, R.310, I.329 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:R.130, G:R.130, G:G.132, G:K.133, G:K.133, G:K.133, G:T.134, G:T.134, G:T.134, G:Q.135, G:R.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Short, J.M. et al., High-resolution structure of the presynaptic RAD51 filament on single-stranded DNA by electron cryo-microscopy. Nucleic Acids Res. (2016)

Release Date

2017-05-03

Peptides

DNA repair protein RAD51 homolog 1: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

DNA repair protein RAD51 homolog 1

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