9Q29 | pdb_00009q29

DX2-CX3 structure capping RAD51 filament

PDB DOI: https://doi.org/10.2210/pdb9Q29/pdb
EM Map EMD-72153: 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: 2.61 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: 346.93 kDa
Atom Count: 21,761
Modeled Residue Count: 2,743
Deposited Residue Count: 3,065
Unique protein chains: 5
Unique nucleic acid chains: 1

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 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% 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: 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% 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	C [auth G], E [auth I], F [auth J], G [auth K], H [auth L]	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% 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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC3	I [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% 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	J [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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43543
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	D [auth H]	30	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 CA [auth R] SDF format, chain N [auth D] SDF format, chain U [auth J] SDF format, chain X [auth K] SDF format, chain Y [auth K] SDF format, chain P [auth G] SDF format, chain M [auth D] MOL2 format, chain CA [auth R] MOL2 format, chain N [auth D] MOL2 format, chain U [auth J] MOL2 format, chain X [auth K] MOL2 format, chain Y [auth K] MOL2 format, chain P [auth G] MOL2 format, chain M [auth D] mmCIF format, chain CA [auth R] mmCIF format, chain N [auth D] mmCIF format, chain U [auth J] mmCIF format, chain X [auth K] mmCIF format, chain Y [auth K] mmCIF format, chain P [auth G] mmCIF format, chain M [auth D]	CA [auth R] M [auth D] N [auth D] P [auth G] U [auth J] CA [auth R], M [auth D], N [auth D], P [auth G], U [auth J], X [auth K], Y [auth K]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain CA [auth R] Focus chain M [auth D] Focus chain N [auth D] Focus chain P [auth G] Focus chain U [auth J] Focus chain X [auth K] Focus chain Y [auth K] Interactions & Density Focus chain CA [auth R] Focus chain M [auth D] Focus chain N [auth D] Focus chain P [auth G] Focus chain U [auth J] Focus chain X [auth K] Focus chain Y [auth K]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth L] SDF format, chain DA [auth R] SDF format, chain EA [auth X] SDF format, chain O [auth D] SDF format, chain R [auth G] SDF format, chain S [auth I] SDF format, chain V [auth J] SDF format, chain W [auth J] SDF format, chain Z [auth K] SDF format, chain T [auth I] SDF format, chain Q [auth G] SDF format, chain L [auth C] SDF format, chain AA [auth K] MOL2 format, chain BA [auth L] MOL2 format, chain DA [auth R] MOL2 format, chain EA [auth X] MOL2 format, chain O [auth D] MOL2 format, chain R [auth G] MOL2 format, chain S [auth I] MOL2 format, chain V [auth J] MOL2 format, chain W [auth J] MOL2 format, chain Z [auth K] MOL2 format, chain T [auth I] MOL2 format, chain Q [auth G] MOL2 format, chain L [auth C] MOL2 format, chain AA [auth K] mmCIF format, chain BA [auth L] mmCIF format, chain DA [auth R] mmCIF format, chain EA [auth X] mmCIF format, chain O [auth D] mmCIF format, chain R [auth G] mmCIF format, chain S [auth I] mmCIF format, chain V [auth J] mmCIF format, chain W [auth J] mmCIF format, chain Z [auth K] mmCIF format, chain T [auth I] mmCIF format, chain Q [auth G] mmCIF format, chain L [auth C] mmCIF format, chain AA [auth K]	AA [auth K] BA [auth L] DA [auth R] EA [auth X] L [auth C] AA [auth K], BA [auth L], DA [auth R], EA [auth X], L [auth C], O [auth D], Q [auth G], R [auth G], S [auth I], T [auth I], V [auth J], W [auth J], Z [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain DA [auth R] Focus chain EA [auth X] Focus chain L [auth C] Focus chain O [auth D] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth I] Focus chain T [auth I] Focus chain V [auth J] Focus chain W [auth J] Focus chain Z [auth K] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain DA [auth R] Focus chain EA [auth X] Focus chain L [auth C] Focus chain O [auth D] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth I] Focus chain T [auth I] Focus chain V [auth J] Focus chain W [auth J] Focus chain Z [auth K]