9SW0 | pdb_00009sw0

XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on a D-loop intermediate

PDB DOI: https://doi.org/10.2210/pdb9SW0/pdb
EM Map EMD-55292: EMDB EMDataResource
NAKB: 9SW0

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Spodoptera frugiperda, Escherichia coli
Mutation(s): No

Deposited: 2025-10-03 Released: 2025-11-12
Deposition Author(s): Greenhough, L.A., West, S.C.
Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom), Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-electron microscopy visualization of RAD51 filament assembly and end-capping by XRCC3-RAD51C-RAD51D-XRCC2.

Greenhough, L.A., Galanti, L., Liang, C.C., Boulton, S.J., West, S.C.

(2025) Science : eaea1546-eaea1546

PubMed: 41196948 Search on PubMed
DOI: https://doi.org/10.1126/science.aea1546
Primary Citation of Related Structures:
9SVX, 9SVY, 9SW0

PubMed Abstract:
Homologous recombination repairs DNA double strand breaks and protects stalled replication forks, but how the five RAD51 paralogs contribute to these processes remains unclear. Mutations in the RAD51 paralogs are linked to heritable breast and ovarian cancers and the cancer-prone disease Fanconi anemia. In this work, we show that the RAD51 paralogs assemble into two distinct heterotetrameric complexes, RAD51B-RAD51C-RAD51D-XRCC2 (RAD51B complex) and XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex). The RAD51B complex promotes dynamic adenosine triphosphate hydrolysis-dependent assembly of RAD51 filaments, whereas the XRCC3 complex stably caps the 5'-termini of RAD51 filaments to promote homologous pairing, as visualized by cryo-electron microscopy. Highly conserved across evolution, these complexes reveal insights into RAD51 filament formation and capping during DNA repair and replication fork stabilization.

Organizational Affiliation

DNA Recombination and Repair Laboratory, The Francis Crick Institute, London, UK.

Macromolecule Content

Total Structure Weight: 456.89 kDa
Atom Count: 28,522
Modeled Residue Count: 3,513
Deposited Residue Count: 3,853
Unique protein chains: 5
Unique nucleic acid chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 4	A [auth B]	328	Homo sapiens	Mutation(s): 0 Gene Names: RAD51D, RAD51L3
UniProt & NIH Common Fund Data Resources
Find proteins for O75771 (Homo sapiens) Explore O75771 Go to UniProtKB: O75771
PHAROS: O75771 GTEx: ENSG00000185379
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75771
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	B [auth F] C [auth G] G [auth E] K [auth H] L [auth I] B [auth F], C [auth G], G [auth E], K [auth H], L [auth I], M [auth J], N [auth K]	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

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC2	H [auth A]	280	Homo sapiens	Mutation(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
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43543
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 3	I [auth C]	376	Homo sapiens	Mutation(s): 0 Gene Names: RAD51C, RAD51L2
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43502
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC3	J [auth D]	346	Homo sapiens	Mutation(s): 0 Gene Names: XRCC3
UniProt & NIH Common Fund Data Resources
Find proteins for O43542 (Homo sapiens) Explore O43542 Go to UniProtKB: O43542
PHAROS: O43542 GTEx: ENSG00000126215
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43542
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
Invading strand DNA (isDNA)	D [auth M]	32	synthetic construct
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
Complementary strand DNA (csDNA)	E [auth N]	59	synthetic construct
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
Exchanged strand DNA (esDNA)	F [auth O]	59	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 AA [auth D] SDF format, chain FA [auth I] SDF format, chain JA [auth J] SDF format, chain O [auth B] SDF format, chain S [auth G] SDF format, chain V [auth E] SDF format, chain P [auth F] SDF format, chain CA [auth H] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth I] MOL2 format, chain JA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain S [auth G] MOL2 format, chain V [auth E] MOL2 format, chain P [auth F] MOL2 format, chain CA [auth H] mmCIF format, chain AA [auth D] mmCIF format, chain FA [auth I] mmCIF format, chain JA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain S [auth G] mmCIF format, chain V [auth E] mmCIF format, chain P [auth F] mmCIF format, chain CA [auth H]	AA [auth D] CA [auth H] FA [auth I] JA [auth J] O [auth B] AA [auth D], CA [auth H], FA [auth I], JA [auth J], O [auth B], P [auth F], S [auth G], V [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth H] Focus chain FA [auth I] Focus chain JA [auth J] Focus chain O [auth B] Focus chain P [auth F] Focus chain S [auth G] Focus chain V [auth E] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth H] Focus chain FA [auth I] Focus chain JA [auth J] Focus chain O [auth B] Focus chain P [auth F] Focus chain S [auth G] Focus chain V [auth E]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain Y [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain Y [auth C]	Y [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain Y [auth C] Interactions & Density Focus chain Y [auth C]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain DA [auth H] SDF format, chain LA [auth K] SDF format, chain Q [auth F] SDF format, chain X [auth E] SDF format, chain T [auth G] SDF format, chain IA [auth J] SDF format, chain HA [auth I] MOL2 format, chain DA [auth H] MOL2 format, chain LA [auth K] MOL2 format, chain Q [auth F] MOL2 format, chain X [auth E] MOL2 format, chain T [auth G] MOL2 format, chain IA [auth J] MOL2 format, chain HA [auth I] mmCIF format, chain DA [auth H] mmCIF format, chain LA [auth K] mmCIF format, chain Q [auth F] mmCIF format, chain X [auth E] mmCIF format, chain T [auth G] mmCIF format, chain IA [auth J] mmCIF format, chain HA [auth I]	DA [auth H] HA [auth I] IA [auth J] LA [auth K] Q [auth F] DA [auth H], HA [auth I], IA [auth J], LA [auth K], Q [auth F], T [auth G], X [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth H] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain LA [auth K] Focus chain Q [auth F] Focus chain T [auth G] Focus chain X [auth E] Interactions & Density Focus chain DA [auth H] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain LA [auth K] Focus chain Q [auth F] Focus chain T [auth G] Focus chain X [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain EA [auth H] SDF format, chain GA [auth I] SDF format, chain R [auth F] SDF format, chain U [auth G] SDF format, chain W [auth E] SDF format, chain Z [auth C] SDF format, chain KA [auth J] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain R [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth C] MOL2 format, chain KA [auth J] mmCIF format, chain BA [auth D] mmCIF format, chain EA [auth H] mmCIF format, chain GA [auth I] mmCIF format, chain R [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth C] mmCIF format, chain KA [auth J]	BA [auth D] EA [auth H] GA [auth I] KA [auth J] R [auth F] BA [auth D], EA [auth H], GA [auth I], KA [auth J], R [auth F], U [auth G], W [auth E], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain KA [auth J] Focus chain R [auth F] Focus chain U [auth G] Focus chain W [auth E] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain KA [auth J] Focus chain R [auth F] Focus chain U [auth G] Focus chain W [auth E] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Greenhough, L.A.

West, S.C.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	CC2098
Medical Research Council (MRC, United Kingdom)	United Kingdom	CC2098
Wellcome Trust	United Kingdom	CC2098
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/W01355X/1