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- EMDB-65955: structure of a 7 nucleotides homology Rad51 D-loop complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65955
Titlestructure of a 7 nucleotides homology Rad51 D-loop complex
Map data
Sample
  • Complex: mRAD51 7-nt homology D-loop
    • Protein or peptide: DNA repair protein RAD51 homolog 1
Keywordshomologous recombination / strand exchange / D-loop / RECOMBINATION / DNA BINDING PROTEIN-DNA complex
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsLuo SC / Ho MC
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-TP-113-L01 to M.C.H Taiwan
CitationJournal: To Be Published
Title: Mechanism of strand exchange of eukaryotic homologous recombination from RAD51 D-loop structures
Authors: Luo SC
History
DepositionAug 23, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65955.png

Downloads & links

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Map

FileDownload / File: emd_65955.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.214
Minimum - Maximum-1.2447524 - 2.5599294
Average (Standard dev.)0.004927528 (±0.058129527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65955_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65955_half_map_2.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 : mRAD51 7-nt homology D-loop

EntireName: mRAD51 7-nt homology D-loop
Components
  • Complex: mRAD51 7-nt homology D-loop
    • Protein or peptide: DNA repair protein RAD51 homolog 1

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Supramolecule #1: mRAD51 7-nt homology D-loop

SupramoleculeName: mRAD51 7-nt homology D-loop / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: mRAD51 protein filament in complex with dsDNA containing a 7-nucleotide homology sequence
Source (natural)Organism: Mus musculus (house mouse)

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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 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMQMQLEAS ADTSVEEESF GPQPISRLEQ CGINANDVKK LEEAGYHTVE AVAYAPKKEL INIKGISEAK ADKILTEAAK LVPMGFTTA TEFHQRRSEI IQITTGSKEL DKLLQGGIET GSITEMFGEF RTGKTQICHT LAVTCQLPID RGGGEGKAMY I DTEGTFRP ...String:
MAMQMQLEAS ADTSVEEESF GPQPISRLEQ CGINANDVKK LEEAGYHTVE AVAYAPKKEL INIKGISEAK ADKILTEAAK LVPMGFTTA TEFHQRRSEI IQITTGSKEL DKLLQGGIET GSITEMFGEF RTGKTQICHT LAVTCQLPID RGGGEGKAMY I DTEGTFRP ERLLAVAERY GLSGSDVLDN VAYARGFNTD HQTQLLYQAE DMMVESRYAL LIVDSATALY RTDYSGRGEL SA RQMHLAR FLRMLLRLAD EFGVAVVITN QVVAQVDGAA MFAADPKKPI GGNIIAHAST TRLYLRKGRG ETRICKIYDS PCL PEAEAM FAINADGVGD AKD

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 40692
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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