9ZZR | pdb_00009zzr

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9ZZR

This is version 1.1 of the entry. See complete history

Literature

Structural insight into how RAD51 paralog exchange regulates RAD51 filament formation.

Rawal, Y.Kwon, Y.Jia, L.Ruben, E.A.Ji, J.H.Guo, L.Stratton, C.M.Nayak, D.Tovar, M.Fang, Q.Jamalruddin, M.A.Zhou, S.Kuppa, S.Syed, S.Jasper, A.M.Katz, J.N.Rogers, C.M.Kaur, H.Samentar, L.Zhao, W.Dray, E.Zhang, F.Stoilova-McPhie, S.Taylor, A.B.Burma, S.Rao, M.K.Libich, D.S.Hromas, R.Mazin, A.V.Jasin, M.Zhou, D.Bernstein, K.A.Greene, E.C.Wasmuth, E.V.Sung, P.Olsen, S.K.

(2026) Nat Struct Mol Biol 33: 768-781

  • DOI: https://doi.org/10.1038/s41594-026-01796-6
  • Primary Citation Related Structures: 
    9OMY, 9OMZ, 9ON2, 9ZZR

  • PubMed Abstract: 

    Homologous recombination (HR) repairs DNA double-strand breaks and stabilizes stressed replication forks, and HR deficiency promotes genome instability and cancer. HR requires assembly of RAD51 nucleoprotein filaments on single-stranded DNA (ssDNA), a process regulated by the human RAD51 paralogs RAD51C, XRCC3, RAD51D and XRCC2. Here, using cryo-electron microscopy, we find that the RAD51-XRCC3-RAD51C complex (RAD51-X3C) assembles into an octamer in which XRCC3 engages the RAD51 DNA-binding surface and RAD51 subunits adopt a misaligned configuration incompatible with filament formation. These features define an autoinhibited RAD51-X3C state that limits nonproductive RAD51 binding to double-stranded DNA or RNA-DNA hybrids while preserving RAD51 availability for ssDNA-dependent strand exchange. We further show that the RAD51D-XRCC2 paralog complex remodels RAD51-X3C into a pentameric RAD51-X3CDX2 assembly by engaging the exposed RAD51C surface and disrupting contacts that stabilize the octamer. This remodeling exposes the RAD51 DNA-binding interface, enhances RAD51-ssDNA filament assembly, and promotes strand exchange on RPA-coated ssDNA, and yields a filament-compatible paralog assembly that integrates into ssDNA-bound RAD51 filaments. Together, these findings establish paralog exchange as a mechanism that converts an autoinhibited RAD51-X3C octamer into an activated RAD51-X3CDX2 pentamer to regulate RAD51 filament formation during HR and replication fork preservation.


  • Organizational Affiliation
    • Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.

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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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 1A [auth R],
B [auth V]
316Homo sapiensMutation(s): 0 
Gene Names: RAD51RAD51ARECA
EC: 3.6.4
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PHAROS:  Q06609
GTEx:  ENSG00000051180 
Entity Groups
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UniProt GroupQ06609
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 1C [auth W],
D [auth O],
E,
F [auth K]
317Homo sapiensMutation(s): 0 
Gene Names: RAD51RAD51ARECA
EC: 3.6.4
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GTEx:  ENSG00000051180 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein XRCC2H [auth X]260Homo sapiensMutation(s): 0 
Gene Names: XRCC2
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PHAROS:  O43543
GTEx:  ENSG00000196584 
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UniProt GroupO43543
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 4I [auth D]313Homo sapiensMutation(s): 0 
Gene Names: RAD51DRAD51L3
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Find proteins for O75771 (Homo sapiens)
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PHAROS:  O75771
GTEx:  ENSG00000185379 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 3J [auth C]339Homo sapiensMutation(s): 0 
Gene Names: RAD51CRAD51L2
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Find proteins for O43502 (Homo sapiens)
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PHAROS:  O43502
GTEx:  ENSG00000108384 
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UniProt GroupO43502
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein XRCC3K [auth B]346Homo sapiensMutation(s): 0 
Gene Names: XRCC3
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PHAROS:  O43542
GTEx:  ENSG00000126215 
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UniProt GroupO43542
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 1L [auth F]314Homo sapiensMutation(s): 0 
Gene Names: RAD51RAD51ARECA
EC: 3.6.4
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Find proteins for Q06609 (Homo sapiens)
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Go to UniProtKB:  Q06609
PHAROS:  Q06609
GTEx:  ENSG00000051180 
Entity Groups
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')G [auth J]23synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
(Subject of Investigation/LOI)

Query on ANP



Download:Ideal Coordinates CCD File
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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant 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
  • Version 1.1: 2026-06-17
    Changes: Data collection, Database references