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- PDB-9qnc: RAD51 filament in complex with magnesium and ATP bound by the RAD... -

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Basic information

Entry
Database: PDB / ID: 9qnc
TitleRAD51 filament in complex with magnesium and ATP bound by the RAD51AP1 C-terminus
Components
  • DNA
  • DNA repair protein RAD51 homolog 1
  • RAD51-associated protein 1
KeywordsDNA BINDING PROTEIN / RAD51 recombinase / RAD51AP1 / filament modulation / homologous recombination / nucleotide hydrolysis
Function / homology
Function and homology information


D-loop DNA binding / positive regulation of reciprocal meiotic recombination / DNA secondary structure binding / presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / cellular response to cisplatin / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening ...D-loop DNA binding / positive regulation of reciprocal meiotic recombination / DNA secondary structure binding / presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / cellular response to cisplatin / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / DNA strand invasion / mitotic recombination / cellular response to camptothecin / lateral element / DNA strand exchange activity / Impaired BRCA2 binding to PALB2 / regulation of DNA damage checkpoint / telomere maintenance via recombination / reciprocal meiotic recombination / single-stranded DNA helicase activity / ATP-dependent DNA damage sensor activity / regulation of double-strand break repair via homologous recombination / HDR through Single Strand Annealing (SSA) / nuclear chromosome / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / Transcriptional Regulation by E2F6 / Impaired BRCA2 binding to RAD51 / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / response to X-ray / ATP-dependent activity, acting on DNA / interstrand cross-link repair / positive regulation of double-strand break repair via homologous recombination / condensed chromosome / DNA polymerase binding / condensed nuclear chromosome / cellular response to ionizing radiation / meiotic cell cycle / cellular response to gamma radiation / protein-DNA complex / PML body / double-strand break repair via homologous recombination / Meiotic recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to toxic substance / HDR through Homologous Recombination (HRR) / single-stranded DNA binding / chromosome / site of double-strand break / double-stranded DNA binding / DNA recombination / chromosome, telomeric region / response to xenobiotic stimulus / mitochondrial matrix / hydrolase activity / DNA repair / chromatin binding / centrosome / DNA damage response / nucleolus / chromatin / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RAD51 interacting motif / : / RAD51 interacting motif / DNA recombination/repair protein Rad51 / : / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. ...RAD51 interacting motif / : / RAD51 interacting motif / DNA recombination/repair protein Rad51 / : / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / SAM-like Helix-hairpin-helix tandem / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA repair protein RAD51 homolog 1 / RAD51-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsKuhlen, L. / Zhang, X.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: RAD51AP1 is a versatile RAD51 modulator.
Authors: Lucas Kuhlen / Bilge Argunhan / Pengtao Liang / Janet Zhong / Laura Masino / Xiaodong Zhang /
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 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-ATP and upon hydrolysis to Mg-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.
History
DepositionMar 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD51 homolog 1
B: RAD51-associated protein 1
C: DNA repair protein RAD51 homolog 1
D: RAD51-associated protein 1
E: DNA repair protein RAD51 homolog 1
F: RAD51-associated protein 1
G: DNA repair protein RAD51 homolog 1
H: RAD51-associated protein 1
I: DNA repair protein RAD51 homolog 1
J: RAD51-associated protein 1
K: DNA repair protein RAD51 homolog 1
L: RAD51-associated protein 1
Z: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,20230
Polymers267,33413
Non-polymers3,86717
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein / Protein/peptide / DNA chain , 3 types, 13 molecules ACEGIKBDFHJLZ

#1: Protein
DNA repair protein RAD51 homolog 1 / HsRAD51 / hRAD51 / RAD51 homolog A


Mass: 37009.125 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD51, RAD51A, RECA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06609
#2: Protein/peptide
RAD51-associated protein 1 / HsRAD51AP1 / RAD51-interacting protein


Mass: 4502.111 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD51AP1, PIR51 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96B01
#3: DNA chain DNA


Mass: 18266.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 17 molecules

#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RAD51 filament in complex with magnesium and ATP bound by the RAD51AP1 C-terminus
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97029 / Symmetry type: POINT
RefinementHighest resolution: 2.98 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316380
ELECTRON MICROSCOPYf_angle_d0.47122228
ELECTRON MICROSCOPYf_dihedral_angle_d18.6436372
ELECTRON MICROSCOPYf_chiral_restr0.0382525
ELECTRON MICROSCOPYf_plane_restr0.0032793

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