9Q25 | pdb_00009q25

DX2-CX3-RAD51 in the closed state

PDB DOI: https://doi.org/10.2210/pdb9Q25/pdb
NAKB: 9Q25
EM Map EMD-72150: 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: 3.24 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: 188.76 kDa
Atom Count: 11,816
Modeled Residue Count: 1,499
Deposited Residue Count: 1,684
Unique protein chains: 5
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 [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% 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 4	B [auth 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	C [auth G]	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC3	E [auth R]	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% 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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC2	F [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: 4
ssDNA (5-mer)	D [auth H]	5	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 I [auth D] SDF format, chain M [auth X] MOL2 format, chain I [auth D] MOL2 format, chain M [auth X] mmCIF format, chain I [auth D] mmCIF format, chain M [auth X]	I [auth D], M [auth X]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth D] Focus chain M [auth X] Interactions & Density Focus chain I [auth D] Focus chain M [auth X]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain K [auth R] MOL2 format, chain G [auth C] MOL2 format, chain K [auth R] mmCIF format, chain G [auth C] mmCIF format, chain K [auth R]	G [auth C], K [auth R]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth C] Focus chain K [auth R] Interactions & Density Focus chain G [auth C] Focus chain K [auth R]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain J [auth D] SDF format, chain L [auth R] SDF format, chain N [auth X] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] MOL2 format, chain L [auth R] MOL2 format, chain N [auth X] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D] mmCIF format, chain L [auth R] mmCIF format, chain N [auth X]	H [auth C], J [auth D], L [auth R], N [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain J [auth D] Focus chain L [auth R] Focus chain N [auth X] Interactions & Density Focus chain H [auth C] Focus chain J [auth D] Focus chain L [auth R] Focus chain N [auth X]