9QNC | pdb_00009qnc

RAD51 filament in complex with magnesium and ATP bound by the RAD51AP1 C-terminus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

RAD51AP1 is a versatile RAD51 modulator.

Kuhlen, L.Argunhan, B.Liang, P.Zhong, J.Masino, L.Zhang, X.

(2025) Proc Natl Acad Sci U S A 122: e2514728122-e2514728122

  • DOI: https://doi.org/10.1073/pnas.2514728122
  • Primary Citation of Related Structures:  
    9QN8, 9QNA, 9QNB, 9QNC

  • PubMed Abstract: 

    RAD51AP1 is an emergent key factor in homologous recombination (HR), the major pathway for accurate repair of DNA double-strand breaks, and in alternative lengthening of telomeres (ALT). Depletion of RAD51AP1 diminishes HR and overexpression is common in cancer, where it is associated with malignancy. Here, we show that RAD51AP1 has a hitherto unknown role in modulating the RAD51 recombinase, the central player in HR. Through a combination of biochemistry and structural biology, we reveal that RAD51AP1 possesses at least three RAD51-binding sites that facilitate its binding across two adjacent RAD51 molecules. We uncover a previously unidentified RAD51-binding mode that stabilizes the RAD51 N-terminal domain and protomer interface in the filaments. We uncover a previously undescribed role for RAD51AP1 in stabilizing RAD51-ssDNA filaments and promoting strand exchange. Our structural data provide the molecular basis for how RAD51AP1 binding induces conformational changes that promote RAD51 DNA association and oligomerization, therefore promoting filament nucleation, stabilization, and strand exchange. Further, we resolved structures of RAD51-ssDNA filaments in the presence of Mg 2+ -ATP and upon hydrolysis to Mg 2+ -ADP, revealing that RAD51 filaments expand upon ATP hydrolysis and explaining how ADP reduces RAD51-DNA binding. Our findings reveal RAD51AP1 as a versatile RAD51 modulator and RAD51 filament remodeler and shed previously unidentified insights into the modulation of HR, which is critical for the maintenance of genome stability.


  • Organizational Affiliation
    • Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College, London SW7 2AZ, United Kingdom.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 1
A, C, E, G, I
A, C, E, G, I, K
339Homo sapiensMutation(s): 0 
Gene Names: RAD51RAD51ARECA
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06609
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RAD51-associated protein 1
B, D, F, H, J
B, D, F, H, J, L
41Homo sapiensMutation(s): 0 
Gene Names: RAD51AP1PIR51
UniProt & NIH Common Fund Data Resources
Find proteins for Q96B01 (Homo sapiens)
Explore Q96B01 
Go to UniProtKB:  Q96B01
PHAROS:  Q96B01
GTEx:  ENSG00000111247 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96B01
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNAM [auth Z]60synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
CA [auth K]
DA [auth K]
N [auth A]
Q [auth C]
T [auth E]
CA [auth K],
DA [auth K],
N [auth A],
Q [auth C],
T [auth E],
W [auth G],
Z [auth I]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
AA [auth I],
O [auth A],
R [auth C],
U [auth E],
X [auth G]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth K],
P [auth C],
S [auth E],
V [auth G],
Y [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references