9Q2A | pdb_00009q2a

BCDX2-CX3-RAD51-RAD51-ssDNA supercomplex

PDB DOI: https://doi.org/10.2210/pdb9Q2A/pdb
NAKB: 9Q2A
EM Map EMD-72154: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-08-14 Released: 2026-03-04
Deposition Author(s): Koo, C.W., Ciferri, C., Yatskevich, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.67 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

Tumor suppressors BCDX2-CX3 supercomplex and DX2-CX3 complex template RAD51 filament formation

Koo, C.W., Ciferri, C., Yatskevich, S.

To be published.

Macromolecule Content

Total Structure Weight: 319.04 kDa
Atom Count: 19,471
Modeled Residue Count: 2,458
Deposited Residue Count: 2,836
Unique protein chains: 6
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 3	A, 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43502
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 2	B	384	Homo sapiens	Mutation(s): 0 Gene Names: RAD51B, RAD51L1, REC2
UniProt & NIH Common Fund Data Resources
Find proteins for O15315 (Homo sapiens) Explore O15315 Go to UniProtKB: O15315
PHAROS: O15315 GTEx: ENSG00000182185
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15315
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 4	D	338	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75771
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	E [auth G], G [auth I]	339	Homo sapiens	Mutation(s): 0 Gene Names: RAD51, RAD51A, RECA 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06609
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC3	H [auth R]	388	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43542
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC2	I [auth X]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43543
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 5
ssDNA (16-mer)	F [auth H]	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R SDF format, chain T [auth X] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R MOL2 format, chain T [auth X] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R mmCIF format, chain T [auth X]	L [auth B], N [auth C], P [auth D], R, T [auth X]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R Focus chain T [auth X] Interactions & Density Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R Focus chain T [auth X]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth R] SDF format, chain U [auth X] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth R] MOL2 format, chain U [auth X] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth R] mmCIF format, chain U [auth X]	K [auth A] M [auth B] O [auth C] Q [auth D] S [auth R] K [auth A], M [auth B], O [auth C], Q [auth D], S [auth R], U [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth R] Focus chain U [auth X] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth R] Focus chain U [auth X]