9ZZR | pdb_00009zzr

Cryo-EM Structure of a RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex

PDB DOI: https://doi.org/10.2210/pdb9ZZR/pdb
EM Map EMD-75014: EMDB EMDataResource
NAKB: 9ZZR

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

Deposited: 2026-01-07 Released: 2026-04-01
Deposition Author(s): Ruben, E.A., Jia, L., 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: 2.95 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 Structure of a RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex

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

To be published.

Macromolecule Content

Total Structure Weight: 393.36 kDa
Atom Count: 26,730
Modeled Residue Count: 3,390
Deposited Residue Count: 3,495
Unique protein chains: 7
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 1	A [auth R], B [auth V]	316	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	C [auth W], D [auth O], E, F [auth K]	317	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC2	H [auth X]	260	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

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 4	I [auth D]	313	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 3	J [auth C]	339	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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC3	K [auth B]	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: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	L [auth F]	314	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 nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3')	G [auth J]	23	synthetic construct
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 W [auth F] SDF format, chain V [auth B] SDF format, chain U [auth C] SDF format, chain T [auth D] SDF format, chain S [auth X] SDF format, chain R [auth K] SDF format, chain Q [auth E] SDF format, chain P [auth E] SDF format, chain O [auth W] SDF format, chain N [auth V] SDF format, chain M [auth R] MOL2 format, chain W [auth F] MOL2 format, chain V [auth B] MOL2 format, chain U [auth C] MOL2 format, chain T [auth D] MOL2 format, chain S [auth X] MOL2 format, chain R [auth K] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth E] MOL2 format, chain O [auth W] MOL2 format, chain N [auth V] MOL2 format, chain M [auth R] mmCIF format, chain W [auth F] mmCIF format, chain V [auth B] mmCIF format, chain U [auth C] mmCIF format, chain T [auth D] mmCIF format, chain S [auth X] mmCIF format, chain R [auth K] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth E] mmCIF format, chain O [auth W] mmCIF format, chain N [auth V] mmCIF format, chain M [auth R]	M [auth R] N [auth V] O [auth W] P [auth E] Q [auth E] M [auth R], N [auth V], O [auth W], P [auth E], Q [auth E], R [auth K], S [auth X], T [auth D], U [auth C], V [auth B], W [auth F]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain M [auth R] Focus chain N [auth V] Focus chain O [auth W] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth K] Focus chain S [auth X] Focus chain T [auth D] Focus chain U [auth C] Focus chain V [auth B] Focus chain W [auth F] Interactions & Density Focus chain M [auth R] Focus chain N [auth V] Focus chain O [auth W] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth K] Focus chain S [auth X] Focus chain T [auth D] Focus chain U [auth C] Focus chain V [auth B] Focus chain W [auth F]