9SVY | pdb_00009svy

XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA

PDB DOI: https://doi.org/10.2210/pdb9SVY/pdb
EM Map EMD-55291: EMDB EMDataResource

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: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM 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.

To be published.

Macromolecule Content

Total Structure Weight: 427.58 kDa
Atom Count: 27,704
Modeled Residue Count: 3,482
Deposited Residue Count: 3,755
Unique protein chains: 5
Unique nucleic acid chains: 2

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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 3	D [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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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC3	E [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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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC2	F [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 1	G [auth E] H [auth F] I [auth G] J [auth H] K [auth I] G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [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: 2
Molecule	Chains	Length	Organism	Image
dN-31nt	B [auth M]	31	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
dN-21nt	C [auth N]	21	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 BA [auth G] SDF format, chain EA [auth H] SDF format, chain HA [auth I] SDF format, chain KA [auth J] SDF format, chain N [auth B] SDF format, chain R [auth D] SDF format, chain T [auth A] SDF format, chain V [auth E] SDF format, chain Y [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain KA [auth J] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth A] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain KA [auth J] mmCIF format, chain N [auth B] mmCIF format, chain R [auth D] mmCIF format, chain T [auth A] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F]	BA [auth G] EA [auth H] HA [auth I] KA [auth J] N [auth B] BA [auth G], EA [auth H], HA [auth I], KA [auth J], N [auth B], R [auth D], T [auth A], V [auth E], Y [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain HA [auth I] Focus chain KA [auth J] Focus chain N [auth B] Focus chain R [auth D] Focus chain T [auth A] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain HA [auth I] Focus chain KA [auth J] Focus chain N [auth B] Focus chain R [auth D] Focus chain T [auth A] Focus chain V [auth E] Focus chain Y [auth F]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain FA [auth H] SDF format, chain IA [auth I] SDF format, chain LA [auth J] SDF format, chain NA [auth K] SDF format, chain X [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain IA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain NA [auth K] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain IA [auth I] mmCIF format, chain LA [auth J] mmCIF format, chain NA [auth K] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth F]	CA [auth G] FA [auth H] IA [auth I] LA [auth J] NA [auth K] CA [auth G], FA [auth H], IA [auth I], LA [auth J], NA [auth K], X [auth E], Z [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain IA [auth I] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain IA [auth I] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain X [auth E] Focus chain Z [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth G] SDF format, chain GA [auth H] SDF format, chain JA [auth I] SDF format, chain MA [auth J] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain U [auth A] SDF format, chain W [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain JA [auth I] MOL2 format, chain MA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth A] MOL2 format, chain W [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain JA [auth I] mmCIF format, chain MA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth A] mmCIF format, chain W [auth E]	AA [auth F] DA [auth G] GA [auth H] JA [auth I] MA [auth J] AA [auth F], DA [auth G], GA [auth H], JA [auth I], MA [auth J], O [auth B], Q [auth C], S [auth D], U [auth A], W [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain JA [auth I] Focus chain MA [auth J] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth A] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain JA [auth I] Focus chain MA [auth J] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth A] Focus chain W [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 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