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- EMDB-52646: CryoEM structure of a RAD51 D-loop -

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Basic information

Entry
Database: EMDB / ID: EMD-52646
TitleCryoEM structure of a RAD51 D-loop
Map datamap
Sample
  • Complex: Complex of RAD51 pre-synaptic filament with donor DNA.
    • Protein or peptide: DNA repair protein RAD51 homolog 1
    • DNA: DNA (26-MER)
    • DNA: DNA (41-MER)
    • DNA: DNA (41-MER)
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsDNA REPAIR / HOMOLOGOUS RECOMBINATION / STRAND EXCHANGE / ATPASE / DNA BINDING PROTEIN
Function / homology
Function and homology information


presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / cellular response to camptothecin / DNA recombinase assembly / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to cisplatin ...presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / cellular response to camptothecin / DNA recombinase assembly / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to cisplatin / DNA strand invasion / cellular response to hydroxyurea / mitotic recombination / lateral element / DNA strand exchange activity / replication-born double-strand break repair via sister chromatid exchange / telomere maintenance via recombination / Impaired BRCA2 binding to PALB2 / regulation of DNA damage checkpoint / single-stranded DNA helicase activity / reciprocal meiotic recombination / 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 / HDR through Single Strand Annealing (SSA) / ATP-dependent DNA damage sensor activity / regulation of double-strand break repair via homologous recombination / nuclear chromosome / Impaired BRCA2 binding to RAD51 / Transcriptional Regulation by E2F6 / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / ATP-dependent activity, acting on DNA / response to X-ray / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / male germ cell nucleus / condensed nuclear chromosome / meiotic cell cycle / cellular response to ionizing radiation / double-strand break repair via homologous recombination / cellular response to gamma radiation / PML body / Meiotic recombination / HDR through Homologous Recombination (HRR) / response to toxic substance / single-stranded DNA binding / site of double-strand break / double-stranded DNA binding / DNA recombination / chromosome, telomeric region / mitochondrial matrix / response to xenobiotic stimulus / DNA repair / centrosome / DNA damage response / chromatin binding / chromatin / nucleolus / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / Helix-hairpin-helix domain ...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 / Helix-hairpin-helix domain / 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
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsPellegrini L / Joudeh L / Appleby RE
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust221892/Z/20/Z United Kingdom
UK Research and Innovation (UKRI)2271086 United Kingdom
CitationJournal: Elife / Year: 2025
Title: Structural mechanism of strand exchange by the RAD51 filament
Authors: Joudeh L / Appleby RE / Maman JD / Pellegrini L
History
DepositionJan 29, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52646.png

Downloads & links

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Map

FileDownload / File: emd_52646.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 416 pix.
= 271.232 Å		0.65 Å/pix.
x 416 pix.
= 271.232 Å		0.65 Å/pix.
x 416 pix.
= 271.232 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.059443682 - 0.17966758
Average (Standard dev.)0.0001816032 (±0.0049728714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 271.232 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map

Fileemd_52646_half_map_1.map
Annotationhalf-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map

Fileemd_52646_half_map_2.map
Annotationhalf-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of RAD51 pre-synaptic filament with donor DNA.

EntireName: Complex of RAD51 pre-synaptic filament with donor DNA.
Components
  • Complex: Complex of RAD51 pre-synaptic filament with donor DNA.
    • Protein or peptide: DNA repair protein RAD51 homolog 1
    • DNA: DNA (26-MER)
    • DNA: DNA (41-MER)
    • DNA: DNA (41-MER)
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Complex of RAD51 pre-synaptic filament with donor DNA.

SupramoleculeName: Complex of RAD51 pre-synaptic filament with donor DNA.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Donor DNA contains a 'mismatch bubble' with a complementary sequence to the invading sequence of the filament.
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
Details: RAD51 protomers A, B, C, D, I contain amino acids 21 to 273 and 282 to 339.
Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.009125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.768257 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DC)(DG)(DT)(DG)(DT)(DG)(DG)(DT)(DA) (DC)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)

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Macromolecule #3: DNA (41-MER)

MacromoleculeName: DNA (41-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.271798 KDa
SequenceString:
(DC)(DC)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DG) (DC)(DT)(DC)(DA)(DA)(DC)(DA)(DT)(DA)(DG) (DG)(DT)(DA)(DC)(DC)(DA)(DC)(DA)(DC) (DG)(DG)(DC)(DG)(DA)(DG)(DC)(DT)(DC)(DG) (DA) (DT)(DG)(DC)(DA)(DC)(DC)(DT)(DC) (DC)(DA)

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Macromolecule #4: DNA (41-MER)

MacromoleculeName: DNA (41-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.474897 KDa
SequenceString:
(DT)(DG)(DG)(DA)(DG)(DG)(DT)(DG)(DC)(DA) (DT)(DC)(DG)(DA)(DG)(DC)(DT)(DC)(DG)(DC) (DG)(DA)(DC)(DA)(DA)(DA)(DC)(DC)(DT) (DT)(DC)(DT)(DA)(DT)(DG)(DT)(DT)(DG)(DA) (DG) (DC)(DG)(DT)(DC)(DA)(DG)(DT)(DC) (DG)(DG)

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 18 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 9 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 8834 / Average exposure time: 1.34 sec. / Average electron dose: 48.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 102679
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-9i62:
CryoEM structure of a RAD51 D-loop

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