9SVY | pdb_00009svy

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Cryo-electron microscopy visualization of RAD51 filament assembly and end-capping by XRCC3-RAD51C-RAD51D-XRCC2.

Greenhough, L.A., Galanti, L., Liang, C.C., Boulton, S.J., West, S.C.

(2025) Science : eaea1546-eaea1546

  • DOI: https://doi.org/10.1126/science.aea1546
  • Primary Citation of Related Structures:  
    9SVX, 9SVY, 9SW0

  • PubMed Abstract: 

    Homologous recombination repairs DNA double strand breaks and protects stalled replication forks, but how the five RAD51 paralogs contribute to these processes remains unclear. Mutations in the RAD51 paralogs are linked to heritable breast and ovarian cancers and the cancer-prone disease Fanconi anemia. In this work, we show that the RAD51 paralogs assemble into two distinct heterotetrameric complexes, RAD51B-RAD51C-RAD51D-XRCC2 (RAD51B complex) and XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex). The RAD51B complex promotes dynamic adenosine triphosphate hydrolysis-dependent assembly of RAD51 filaments, whereas the XRCC3 complex stably caps the 5'-termini of RAD51 filaments to promote homologous pairing, as visualized by cryo-electron microscopy. Highly conserved across evolution, these complexes reveal insights into RAD51 filament formation and capping during DNA repair and replication fork stabilization.

    • Organizational Affiliation: 
    • DNA Recombination and Repair Laboratory, The Francis Crick Institute, London, UK.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 4A [auth B]328Homo sapiensMutation(s): 0 
Gene Names: RAD51D, RAD51L3
UniProt & NIH Common Fund Data Resources
Find proteins for O75771 (Homo sapiens)
Explore O75771 
Go to UniProtKB:  O75771
PHAROS:  O75771
GTEx:  ENSG00000185379 
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UniProt GroupO75771
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 3D [auth C]376Homo sapiensMutation(s): 0 
Gene Names: RAD51C, RAD51L2
UniProt & NIH Common Fund Data Resources
Find proteins for O43502 (Homo sapiens)
Explore O43502 
Go to UniProtKB:  O43502
PHAROS:  O43502
GTEx:  ENSG00000108384 
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UniProt GroupO43502
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein XRCC3E [auth D]346Homo sapiensMutation(s): 0 
Gene Names: XRCC3
UniProt & NIH Common Fund Data Resources
Find proteins for O43542 (Homo sapiens)
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Go to UniProtKB:  O43542
PHAROS:  O43542
GTEx:  ENSG00000126215 
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UniProt GroupO43542
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein XRCC2F [auth A]280Homo sapiensMutation(s): 0 
Gene Names: XRCC2
UniProt & NIH Common Fund Data Resources
Find proteins for O43543 (Homo sapiens)
Explore O43543 
Go to UniProtKB:  O43543
PHAROS:  O43543
GTEx:  ENSG00000196584 
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UniProt GroupO43543
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 1339Homo sapiensMutation(s): 0 
Gene Names: RAD51, RAD51A, RECA
UniProt & NIH Common Fund Data Resources
Find proteins for Q06609 (Homo sapiens)
Explore Q06609 
Go to UniProtKB:  Q06609
PHAROS:  Q06609
GTEx:  ENSG00000051180 
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UniProt GroupQ06609
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Entity ID: 2
MoleculeChains LengthOrganismImage
dN-31ntB [auth M]31synthetic construct
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Entity ID: 3
MoleculeChains LengthOrganismImage
dN-21ntC [auth N]21synthetic construct
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP
Download Ideal Coordinates CCD File 
BA [auth G]
EA [auth H]
HA [auth I]
KA [auth J]
N [auth B]
BA [auth G],
EA [auth H],
HA [auth I],
KA [auth J],
N [auth B],
R [auth D],
T [auth A],
V [auth E],
Y [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP
Download Ideal Coordinates CCD File 
P [auth C]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CA (Subject of Investigation/LOI)
Query on CA
Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
IA [auth I]
LA [auth J]
NA [auth K]
CA [auth G],
FA [auth H],
IA [auth I],
LA [auth J],
NA [auth K],
X [auth E],
Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
AA [auth F]
DA [auth G]
GA [auth H]
JA [auth I]
MA [auth J]
AA [auth F],
DA [auth G],
GA [auth H],
JA [auth I],
MA [auth J],
O [auth B],
Q [auth C],
S [auth D],
U [auth A],
W [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomCC2098
Medical Research Council (MRC, United Kingdom)United KingdomCC2098
Wellcome TrustUnited KingdomCC2098
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/W01355X/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references