8RCD

RAD51 nucleoprotein filament on abasic single-stranded DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

RAD51 protects abasic sites to prevent replication fork breakage.

Hanthi, Y.W.Ramirez-Otero, M.A.Appleby, R.De Antoni, A.Joudeh, L.Sannino, V.Waked, S.Ardizzoia, A.Barra, V.Fachinetti, D.Pellegrini, L.Costanzo, V.

(2024) Mol Cell 84: 3026-3043.e11

  • DOI: https://doi.org/10.1016/j.molcel.2024.07.004
  • Primary Citation of Related Structures:  
    8RCD, 8RCF

  • PubMed Abstract: 

    Abasic sites are DNA lesions repaired by base excision repair. Cleavage of unrepaired abasic sites in single-stranded DNA (ssDNA) can lead to chromosomal breakage during DNA replication. How rupture of abasic DNA is prevented remains poorly understood. Here, using cryoelectron microscopy (cryo-EM), Xenopus laevis egg extracts, and human cells, we show that RAD51 nucleofilaments specifically recognize and protect abasic sites, which increase RAD51 association rate to DNA. In the absence of BRCA2 or RAD51, abasic sites accumulate as a result of DNA base methylation, oxidation, and deamination, inducing abasic ssDNA gaps that make replicating DNA fibers sensitive to APE1. RAD51 assembled on abasic DNA prevents abasic site cleavage by the MRE11-RAD50 complex, suppressing replication fork breakage triggered by an excess of abasic sites or POLθ polymerase inhibition. Our study highlights the critical role of BRCA2 and RAD51 in safeguarding against unrepaired abasic sites in DNA templates stemming from base alterations, ensuring genomic stability.


  • Organizational Affiliation

    IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 1
A, B, C, D, E
A, B, C, D, E, F, G, H
339Homo sapiensMutation(s): 0 
Gene Names: RAD51RAD51ARECA
UniProt & NIH Common Fund Data Resources
Find proteins for Q06609 (Homo sapiens)
Explore Q06609 
Go to UniProtKB:  Q06609
PHAROS:  Q06609
GTEx:  ENSG00000051180 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06609
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*GP*(3DR)P*AP*TP*(3DR)P*CP*AP*(3DR)P*TP*GP*(3DR)P*TP*AP*(3DR)P*AP*CP*(3DR)P*TP*GP*(3DR)P*GP*C)-3')23Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
J [auth A]
N [auth B]
Q [auth C]
CA [auth G],
FA [auth H],
J [auth A],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
DA [auth G]
EA [auth G]
GA [auth H]
AA [auth F],
BA [auth F],
DA [auth G],
EA [auth G],
GA [auth H],
K [auth A],
L [auth A],
M [auth A],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
X [auth E],
Y [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.21rc1-4985

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom221892/Z/20/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Data collection, Database references