9OMY | pdb_00009omy

Cryo-EM structure of an octameric RAD51-XRCC3-RAD51C (RAD51-X3C) complex

PDB DOI: https://doi.org/10.2210/pdb9OMY/pdb
EM Map EMD-70624: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): No

Deposited: 2025-05-14 Released: 2026-04-01
Deposition Author(s): Jia, L., Ruben, E.A., Olsen, S.K., Wasmuth, E.V., Rawal, Y., Kwon, Y., Sung, P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9OMY

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

Literature

Cryo-EM structure of an octameric RAD51-XRCC3-RAD51C (RAD51-X3C) complex.

Jia, L., Ruben, E.A., Olsen, S.K., Wasmuth, E.A., Rawal, Y., Kwon, Y., Sung, P.

To be published.

Macromolecule Content

Total Structure Weight: 311.36 kDa
Atom Count: 18,444
Modeled Residue Count: 2,368
Deposited Residue Count: 2,800
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	A, B, E [auth D], F [auth E]	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

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 3	C, G [auth F]	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

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC3	D [auth X], H [auth G]	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain N [auth G] SDF format, chain M [auth F] SDF format, chain L [auth D] SDF format, chain K [auth X] SDF format, chain J [auth C] SDF format, chain I [auth A] MOL2 format, chain N [auth G] MOL2 format, chain M [auth F] MOL2 format, chain L [auth D] MOL2 format, chain K [auth X] MOL2 format, chain J [auth C] MOL2 format, chain I [auth A] mmCIF format, chain N [auth G] mmCIF format, chain M [auth F] mmCIF format, chain L [auth D] mmCIF format, chain K [auth X] mmCIF format, chain J [auth C] mmCIF format, chain I [auth A]	I [auth A] J [auth C] K [auth X] L [auth D] M [auth F] I [auth A], J [auth C], K [auth X], L [auth D], M [auth F], N [auth G]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth X] Focus chain L [auth D] Focus chain M [auth F] Focus chain N [auth G] Interactions & Density Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth X] Focus chain L [auth D] Focus chain M [auth F] Focus chain N [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-04-01
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.