8R64

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

PDB DOI: https://doi.org/10.2210/pdb8R64/pdb
EM Map EMD-18946: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-11-20 Released: 2024-09-04
Deposition Author(s): Carver, A., Yates, L.A., Zhang, X.
Funding Organization(s): Breast Cancer Now, Wellcome Trust

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

This is version 1.0 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.

(2024) bioRxiv

PubMed: 39071279 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1101/2024.07.16.603765
Primary Citation of 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 and protecting genome integrity, forms filaments on DNA. RAD51 filaments are tightly regulated. One of these regulators is FIGNL1, that prevents persistent RAD51 foci post-damage and genotoxic chromatin association in cells. The cryogenic electron microscopy structure of FIGNL1 in complex with RAD51 reveals that the FIGNL1 forms a non-planar hexamer and RAD51 N-terminus is enclosed 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 DNA 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
Modelled Residue Count: 1,765
Deposited Residue Count: 2,841
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fidgetin-like protein 1	A [auth B] B [auth C] C [auth D] D [auth E] E [auth F] A [auth B], B [auth C], C [auth D], D [auth E], E [auth F], F [auth A]	417	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6PIW4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	G	339	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06609
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain S [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain S [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain S [auth A]	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		Interactions Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain S [auth A] Interactions & Density Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain S [auth A]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain Q [auth F] MOL2 format, chain Q [auth F] mmCIF format, chain Q [auth F]	Q [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain Q [auth F] Interactions & Density Focus chain Q [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain N [auth E] SDF format, chain P [auth F] SDF format, chain R [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] MOL2 format, chain R [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E] mmCIF format, chain P [auth F] mmCIF format, chain R [auth A]	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		Interactions Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain R [auth A] Interactions & Density Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain R [auth A]