8OUZ

Human RAD51B-RAD51C-RAD51D-XRCC2 (BCDX2) complex, 2.2 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and function of the RAD51B-RAD51C-RAD51D-XRCC2 tumour suppressor.

Greenhough, L.A.Liang, C.C.Belan, O.Kunzelmann, S.Maslen, S.Rodrigo-Brenni, M.C.Anand, R.Skehel, M.Boulton, S.J.West, S.C.

(2023) Nature 619: 650-657

  • DOI: https://doi.org/10.1038/s41586-023-06179-1
  • Primary Citation of Related Structures:  
    8OUY, 8OUZ

  • PubMed Abstract: 

    Homologous recombination is a fundamental process of life. It is required for the protection and restart of broken replication forks, the repair of chromosome breaks and the exchange of genetic material during meiosis. Individuals with mutations in key recombination genes, such as BRCA2 (also known as FANCD1), or the RAD51 paralogues RAD51B, RAD51C (also known as FANCO), RAD51D, XRCC2 (also known as FANCU) and XRCC3, are predisposed to breast, ovarian and prostate cancers 1-10 and the cancer-prone syndrome Fanconi anaemia 11-13 . The BRCA2 tumour suppressor protein-the product of BRCA2-is well characterized, but the cellular functions of the RAD51 paralogues remain unclear. Genetic knockouts display growth defects, reduced RAD51 focus formation, spontaneous chromosome abnormalities, sensitivity to PARP inhibitors and replication fork defects 14,15 , but the precise molecular roles of RAD51 paralogues in fork stability, DNA repair and cancer avoidance remain unknown. Here we used cryo-electron microscopy, AlphaFold2 modelling and structural proteomics to determine the structure of the RAD51B-RAD51C-RAD51D-XRCC2 complex (BCDX2), revealing that RAD51C-RAD51D-XRCC2 mimics three RAD51 protomers aligned within a nucleoprotein filament, whereas RAD51B is highly dynamic. Biochemical and single-molecule analyses showed that BCDX2 stimulates the nucleation and extension of RAD51 filaments-which are essential for recombinational DNA repair-in reactions that depend on the coupled ATPase activities of RAD51B and RAD51C. Our studies demonstrate that BCDX2 orchestrates RAD51 assembly on single stranded DNA for replication fork protection and double strand break repair, in reactions that are critical for tumour avoidance.


  • Organizational Affiliation

    The Francis Crick Institute, London, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 2350Homo sapiensMutation(s): 0 
Gene Names: RAD51BRAD51L1REC2
UniProt & NIH Common Fund Data Resources
Find proteins for O15315 (Homo sapiens)
Explore O15315 
Go to UniProtKB:  O15315
PHAROS:  O15315
GTEx:  ENSG00000182185 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15315
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 3376Homo sapiensMutation(s): 0 
Gene Names: RAD51CRAD51L2
UniProt & NIH Common Fund Data Resources
Find proteins for O43502 (Homo sapiens)
Explore O43502 
Go to UniProtKB:  O43502
PHAROS:  O43502
GTEx:  ENSG00000108384 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43502
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 4328Homo sapiensMutation(s): 0 
Gene Names: RAD51DRAD51L3
UniProt & NIH Common Fund Data Resources
Find proteins for O75771 (Homo sapiens)
Explore O75771 
Go to UniProtKB:  O75771
PHAROS:  O75771
GTEx:  ENSG00000185379 
Entity Groups  
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UniProt GroupO75771
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein XRCC2280Homo 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 
Entity Groups  
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UniProt GroupO43543
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
G [auth C],
I [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
E [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
F [auth B],
H [auth C],
J [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.2
MODEL REFINEMENTCoot0.9.8.7

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/W01355X/1
Cancer Research UKUnited KingdomCC2098
Medical Research Council (MRC, United Kingdom)United KingdomCC2098
Wellcome TrustUnited KingdomCC2098
European Research Council (ERC)European UnionERC-ADG-666400

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2023-08-02
    Changes: Database references
  • Version 1.3: 2024-07-24
    Changes: Data collection, Refinement description