SMTL ID : 9svy.1

XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.60 Å

Oligo State

hetero-1-1-1-1-7-mer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: G.108, P.109, G.110, S.111, G.112, K.113, T.114, Q.115, N.138, R.145, R.291 Chain D: H.307, K.328, S.329, P.330, S.331, Q.332, K.333, E.334 Ligands: MG.2 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:G.110, A:G.110, A:S.111, A:G.112, A:K.113, A:T.114, A:T.114, A:Q.115, A:Q.115, A:R.291, D:E.334 Salt bridges: A:K.113, A:K.113, D:H.307, D:K.328 ATP.5: 22 residues within 4Å: Chain E: R.108, S.109, S.110, A.111, G.112, K.113, T.114, Q.115, E.143, R.150, R.313, I.332 Chain G: H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Ligands: MG.6, CA.11 17 PLIP interactions: 4 interactions with chain G, 13 interactions with chain E Hydrogen bonds: G:L.320, G:E.322, G:E.322, E:S.110, E:S.110, E:A.111, E:G.112, E:K.113, E:T.114, E:T.114, E:T.114, E:Q.115, E:Q.115, E:R.313 Salt bridges: G:H.294, E:K.113, E:K.113 ATP.7: 18 residues within 4Å: Chain A: K.297, S.298, R.300, Q.301, P.302, T.303 Chain F: E.50, G.51, T.52, G.53, K.54, T.55, E.56, R.91, I.272, G.273, E.274 Ligands: MG.8 21 PLIP interactions: 15 interactions with chain F, 6 interactions with chain A Hydrogen bonds: F:E.50, F:G.51, F:G.51, F:T.52, F:G.53, F:K.54, F:T.55, F:T.55, F:T.55, F:E.56, F:H.86, F:R.91, F:R.91, A:R.300, A:T.303, A:T.303 Salt bridges: F:K.54, F:K.54, A:K.297, A:K.297, A:K.297 ATP.9: 21 residues within 4Å: Chain G: E.128, F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, R.310, I.329, N.330 Chain H: H.294, D.316, S.317, P.318, C.319, L.320, P.321 Ligands: MG.10, CA.13 14 PLIP interactions: 12 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:R.130, G:T.131, G:T.131, G:G.132, G:K.133, G:T.134, G:T.134, G:Q.135, G:Q.135, G:R.310, H:C.319 Salt bridges: G:K.133, G:K.133, H:H.294 ATP.12: 22 residues within 4Å: Chain H: E.128, F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, N.330 Chain I: H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Ligands: MG.14, CA.16 18 PLIP interactions: 12 interactions with chain H, 6 interactions with chain I Hydrogen bonds: H:R.130, H:T.131, H:T.131, H:G.132, H:K.133, H:T.134, H:T.134, H:Q.135, H:Q.135, H:R.310, I:H.294, I:C.319, I:E.322, I:E.322, I:E.322 Salt bridges: H:K.133, H:K.133, I:H.294 ATP.15: 22 residues within 4Å: Chain I: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330 Chain J: H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Ligands: MG.17, CA.19 17 PLIP interactions: 4 interactions with chain J, 13 interactions with chain I Hydrogen bonds: J:A.293, J:C.319, J:E.322, I:R.130, I:T.131, I:G.132, I:K.133, I:T.134, I:T.134, I:T.134, I:Q.135, I:Q.135, I:E.163, I:R.310 Salt bridges: J:H.294, I:K.133, I:K.133 ATP.18: 23 residues within 4Å: Chain J: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330 Chain K: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Ligands: MG.20, CA.22 17 PLIP interactions: 12 interactions with chain J, 5 interactions with chain K Hydrogen bonds: J:R.130, J:T.131, J:G.132, J:K.133, J:T.134, J:T.134, J:Q.135, J:Q.135, J:E.163, J:R.310, K:C.319, K:E.322, K:E.322, K:E.322 Salt bridges: J:K.133, J:K.133, K:H.294 ATP.21: 23 residues within 4Å: Chain K: E.128, 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 L: H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Ligands: MG.23, CA.25 18 PLIP interactions: 13 interactions with chain K, 5 interactions with chain L Hydrogen bonds: K:R.130, K:T.131, K:T.131, K:G.132, K:K.133, K:T.134, K:T.134, K:Q.135, K:Q.135, K:R.170, K:R.310, L:C.319, L:E.322, L:E.322, L:E.322 Salt bridges: K:K.133, K:K.133, L:H.294 ATP.24: 24 residues within 4Å: Chain L: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Chain M: H.294, Y.315, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Ligands: MG.26, CA.27 17 PLIP interactions: 13 interactions with chain L, 4 interactions with chain M Hydrogen bonds: L:R.130, L:T.131, L:T.131, L:G.132, L:K.133, L:T.134, L:T.134, L:Q.135, L:Q.135, L:E.163, L:R.310, M:C.319, M:E.322, M:E.322 Salt bridges: L:K.133, L:K.133, M:H.294

10 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.114 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.114 MG.4: 2 residues within 4Å: Chain D: T.132 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.132 MG.6: 3 residues within 4Å: Chain E: T.114, E.143 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.114 MG.8: 2 residues within 4Å: Chain F: T.55 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain G: T.134 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.134 MG.14: 3 residues within 4Å: Chain H: T.134, E.163 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.134 MG.17: 3 residues within 4Å: Chain I: T.134, E.163 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.134 MG.20: 3 residues within 4Å: Chain J: T.134, E.163 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.134 MG.23: 2 residues within 4Å: Chain K: T.134 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.134 MG.26: 3 residues within 4Å: Chain L: T.134, E.163 Ligands: ATP.24 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.134

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 18 residues within 4Å: Chain D: A.126, G.128, V.129, G.130, K.131, T.132, Q.133, R.168, R.322, I.341 Chain E: S.319, A.320, P.321, H.322, L.323, P.324, P.325 Ligands: MG.4 10 PLIP interactions: 1 interactions with chain E, 9 interactions with chain D Hydrogen bonds: E:H.322, D:G.128, D:G.128, D:V.129, D:G.130, D:K.131, D:T.132, D:Q.133, D:R.322 Salt bridges: D:K.131

7 x CA: CALCIUM ION(Non-covalent)

CA.11: 5 residues within 4Å: Chain G: A.293, H.294, S.296, D.316 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:S.296, G:D.316 CA.13: 5 residues within 4Å: Chain H: A.293, H.294, S.296, D.316 Ligands: ATP.9 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:A.293, H:S.296, H:D.316 CA.16: 5 residues within 4Å: Chain I: A.293, H.294, S.296, D.316 Ligands: ATP.12 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:A.293, I:S.296, I:D.316 CA.19: 5 residues within 4Å: Chain J: A.293, H.294, S.296, D.316 Ligands: ATP.15 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:A.293, J:S.296, J:D.316 CA.22: 5 residues within 4Å: Chain K: A.293, H.294, S.296, D.316 Ligands: ATP.18 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:A.293, K:S.296 CA.25: 5 residues within 4Å: Chain L: A.293, H.294, S.296, D.316 Ligands: ATP.21 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:A.293, L:S.296, L:D.316 CA.27: 5 residues within 4Å: Chain M: A.293, H.294, S.296, D.316 Ligands: ATP.24 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:A.293, M:S.296, M:D.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Greenhough, L.A. et al., Cryo-EM visualization of RAD51 filament assembly and end-cappingby XRCC3-RAD51C-RAD51D-XRCC2. To Be Published

Release Date

2025-11-12

Peptides

DNA repair protein RAD51 homolog 4: A
DNA repair protein RAD51 homolog 3: D
DNA repair protein XRCC3: E
DNA repair protein XRCC2: F
DNA repair protein RAD51 homolog 1: GHIJKLM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
C

E
D

F
A

G
E

H
F

I
G

J
H

K
I

L
J

M
K

DNA repair protein RAD51 homolog 4

DNA repair protein RAD51 homolog 3

DNA repair protein XRCC3

DNA repair protein XRCC2

DNA repair protein RAD51 homolog 1

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