8BSC

CryoEM structure of the RAD51 nucleoprotein filament in the presence of ADP and Ca2+


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A metal ion-dependent mechanism of RAD51 nucleoprotein filament disassembly.

Appleby, R.Bollschweiler, D.Chirgadze, D.Y.Joudeh, L.Pellegrini, L.

(2023) iScience 26: 106689-106689

  • DOI: https://doi.org/10.1016/j.isci.2023.106689
  • Primary Citation of Related Structures:  
    8BQ2, 8BR2, 8BSC

  • PubMed Abstract: 

    The RAD51 ATPase polymerizes on single-stranded DNA to form nucleoprotein filaments (NPFs) that are critical intermediates in the reaction of homologous recombination. ATP binding maintains the NPF in a competent conformation for strand pairing and exchange. Once strand exchange is completed, ATP hydrolysis licenses the filament for disassembly. Here we show that the ATP-binding site of the RAD51 NPF contains a second metal ion. In the presence of ATP, the metal ion promotes the local folding of RAD51 into the conformation required for DNA binding. The metal ion is absent in the ADP-bound RAD51 filament, that rearranges in a conformation incompatible with DNA binding. The presence of the second metal ion explains how RAD51 couples the nucleotide state of the filament to DNA binding. We propose that loss of the second metal ion upon ATP hydrolysis drives RAD51 dissociation from the DNA and weakens filament stability, contributing to NPF disassembly.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 1339Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
I [auth D]
K [auth A]
M [auth B]
O [auth C]
Q [auth E]
I [auth D],
K [auth A],
M [auth B],
O [auth C],
Q [auth E],
S [auth F],
U [auth G]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
H [auth D]
J [auth A]
L [auth B]
N [auth C]
P [auth E]
H [auth D],
J [auth A],
L [auth B],
N [auth C],
P [auth E],
R [auth F],
T [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIXdev-4707

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: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references