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- EMDB-53239: RAD51 filament in complex with calcium and ATP bound by the RAD51... -

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Entry
Database: EMDB / ID: EMD-53239
TitleRAD51 filament in complex with calcium and ATP bound by the RAD51AP1 C-terminus
Map data
Sample
  • Complex: RAD51 filament in complex with calcium and ATP bound by the RAD51AP1 C-terminus
    • Protein or peptide: DNA repair protein RAD51 homolog 1
    • Protein or peptide: RAD51-associated protein 1
    • DNA: DNA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CALCIUM ION
  • Ligand: POTASSIUM ION
KeywordsRAD51 recombinase / RAD51AP1 / filament modulation / homologous recombination / nucleotide hydrolysis / DNA BINDING PROTEIN
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 / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / cellular response to cisplatin / double-strand break repair involved in meiotic recombination ...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 / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / cellular response to cisplatin / double-strand break repair involved in meiotic recombination / DNA recombinase assembly / nuclear ubiquitin ligase complex / cellular response to camptothecin / DNA strand invasion / mitotic recombination / lateral element / Impaired BRCA2 binding to PALB2 / DNA strand exchange activity / telomere maintenance via recombination / reciprocal meiotic recombination / response to X-ray / regulation of double-strand break repair via homologous recombination / ATP-dependent DNA damage sensor activity / regulation of DNA damage checkpoint / 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) / HDR through Single Strand Annealing (SSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / Transcriptional Regulation by E2F6 / nuclear chromosome / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / 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 / nucleosome binding / meiotic cell cycle / replication fork processing / cellular response to ionizing radiation / condensed nuclear chromosome / response to toxic substance / double-strand break repair via homologous recombination / cellular response to gamma radiation / protein-DNA complex / PML body / Meiotic recombination / HDR through Homologous Recombination (HRR) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / site of double-strand break / DNA recombination / double-stranded DNA binding / chromosome, telomeric region / response to xenobiotic stimulus / mitochondrial matrix / DNA repair / chromosome / centrosome / chromatin binding / DNA damage response / nucleolus / chromatin / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / 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. / DNA recombination and repair protein RecA-like, ATP-binding domain ...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
DNA repair protein RAD51 homolog 1 / RAD51-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsKuhlen L / Zhang X
Funding support United Kingdom, 1 items
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, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53239.png

Downloads & links

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Map

FileDownload / File: emd_53239.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.448
Minimum - Maximum-2.3199267 - 3.7573419
Average (Standard dev.)0.0068300916 (±0.13379577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53239_msk_1.map
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Additional map: density modified with EMReady

Fileemd_53239_additional_1.map
Annotationdensity modified with EMReady
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Additional map: unsharpened map

Fileemd_53239_additional_2.map
Annotationunsharpened map
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Half map: #2

Fileemd_53239_half_map_1.map
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Half map: #1

Fileemd_53239_half_map_2.map
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Sample components

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Entire : RAD51 filament in complex with calcium and ATP bound by the RAD51...

EntireName: RAD51 filament in complex with calcium and ATP bound by the RAD51AP1 C-terminus
Components
  • Complex: RAD51 filament in complex with calcium and ATP bound by the RAD51AP1 C-terminus
    • Protein or peptide: DNA repair protein RAD51 homolog 1
    • Protein or peptide: RAD51-associated protein 1
    • DNA: DNA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CALCIUM ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: RAD51 filament in complex with calcium and ATP bound by the RAD51...

SupramoleculeName: RAD51 filament in complex with calcium and ATP bound by the RAD51AP1 C-terminus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA repair protein RAD51 homolog 1

MacromoleculeName: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.009125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAMQMQLEAN ADTSVEEESF GPQPISRLEQ CGINANDVKK LEEAGFHTVE AVAYAPKKEL INIKGISEAK ADKILAEAAK LVPMGFTTA TEFHQRRSEI IQITTGSKEL DKLLQGGIET GSITEMFGEF RTGKTQICHT LAVTCQLPID RGGGEGKAMY I DTEGTFRP ...String:
MAMQMQLEAN ADTSVEEESF GPQPISRLEQ CGINANDVKK LEEAGFHTVE AVAYAPKKEL INIKGISEAK ADKILAEAAK LVPMGFTTA TEFHQRRSEI IQITTGSKEL DKLLQGGIET GSITEMFGEF RTGKTQICHT LAVTCQLPID RGGGEGKAMY I DTEGTFRP ERLLAVAERY GLSGSDVLDN VAYARAFNTD HQTQLLYQAS AMMVESRYAL LIVDSATALY RTDYSGRGEL SA RQMHLAR FLRMLLRLAD EFGVAVVITN QVVAQVDGAA MFAADPKKPI GGNIIAHAST TRLYLRKGRG ETRICKIYDS PCL PEAEAM FAINADGVGD AKD

UniProtKB: DNA repair protein RAD51 homolog 1

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Macromolecule #2: RAD51-associated protein 1

MacromoleculeName: RAD51-associated protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.891938 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPMVRPVRHK KPVNYSQFDH SDSDDDFVSA TVPLNKKSRT APKELKQDKP KPNLNNLRKE EIPVQEKTPK KRLPEGTFSI PASAVPCTK MALDDKLYQR DLEVALALSV KELPTVTTNV QNSQDKSIEK HGSSKIETMN KSPHISNCSV ASDYLDLDKI T VEDDVGGV ...String:
GPMVRPVRHK KPVNYSQFDH SDSDDDFVSA TVPLNKKSRT APKELKQDKP KPNLNNLRKE EIPVQEKTPK KRLPEGTFSI PASAVPCTK MALDDKLYQR DLEVALALSV KELPTVTTNV QNSQDKSIEK HGSSKIETMN KSPHISNCSV ASDYLDLDKI T VEDDVGGV QGKRKAASKA AAQQRKILLE GSDGDSANDT EPDFAPGEDS EDDSDFCESE DNDEDFSMRK SKVKEIKKKE VK VKSPVEK KEKKSKSKCN ALVTSVDSAP AAVKSESQSL PKKVSLSSDT TRKPLEIRSP SAESKKPKWV PPAASGGSRS SSS PLVVVS VKSPNQSLRL GLSRLARVKP LHPNATSTAA LEHHHHHH

UniProtKB: RAD51-associated protein 1

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Macromolecule #3: DNA

MacromoleculeName: DNA / type: dna / ID: 3
Details: mixed oligomer GCTCCTCTAGACTCGAGGAATTCGGTACCCCGGGTTCGAAATCGATAAGC modelled as poly dT
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.343091 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 7 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 7 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 7 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137283
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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