8R64 | pdb_00008r64

Cryo-EM structure of the FIGNL1 AAA hexamer bound to RAD51


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8R64

This is version 1.3 of the entry. See complete history

Literature

Molecular basis of FIGNL1 in dissociating RAD51 from DNA and chromatin.

Carver, A.Yu, T.Y.Yates, L.A.White, T.Wang, R.Lister, K.Jasin, M.Zhang, X.

(2025) Science 387: 426-431

  • DOI: https://doi.org/10.1126/science.adr7920
  • Primary Citation Related Structures: 
    8R64

  • PubMed Abstract: 

    Maintaining genome integrity is an essential and challenging process. RAD51 recombinase, the central player of several crucial processes in repairing DNA and protecting genome integrity, forms filaments on DNA, which are tightly regulated. One of these RAD51 regulators is FIGNL1, that prevents persistent RAD51 foci without or after DNA damage and genotoxic chromatin association in cells. The cryogenic electron microscopy structure of FIGNL1 in complex with RAD51 reveals that FIGNL1 forms a non-planar hexamer and RAD51 N terminus enclosure in the FIGNL1 hexamer pore. Mutations in pore loop or catalytic residues of FIGNL1 render it defective in filament disassembly and are lethal in mouse embryonic stem cells. Our study reveals a unique mechanism for removing RAD51 from bound substrates and provides the molecular basis for FIGNL1 in maintaining genome stability.


  • Organizational Affiliation
    • DNA Processing Machines Laboratory, Francis Crick Institute, London, UK.

Macromolecule Content 

  • Total Structure Weight: 317.05 kDa 
  • Atom Count: 13,429 
  • Modeled Residue Count: 1,765 
  • Deposited Residue Count: 2,841 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fidgetin-like protein 1417Homo sapiensMutation(s): 1 
Gene Names: FIGNL1
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PIW4 (Homo sapiens)
Explore Q6PIW4 
Go to UniProtKB:  Q6PIW4
PHAROS:  Q6PIW4
GTEx:  ENSG00000132436 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PIW4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 1339Homo sapiensMutation(s): 0 
Gene Names: RAD51RAD51ARECA
EC: 3.6.4
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
I [auth B],
K [auth C],
M [auth D],
O [auth E],
S [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
(Subject of Investigation/LOI)

Query on ADP



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

Query on MG



Download:Ideal Coordinates CCD File
H [auth B]
J [auth C]
L [auth D]
N [auth E]
P [auth F]
H [auth B],
J [auth C],
L [auth D],
N [auth E],
P [auth F],
R [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Breast Cancer NowUnited Kingdom--
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2025-01-08
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-02-05
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-02
    Changes: Data collection