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- EMDB-53921: RecA 12-monomer mini-filament bound to dsDNA with 7-nt homology a... -

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Basic information

Entry
Database: EMDB / ID: EMD-53921
TitleRecA 12-monomer mini-filament bound to dsDNA with 7-nt homology at 250ms using time-resolved cryo-EM
Map dataConsensus refinement of (RecAmini-filament dsDNA7-nt)250ms
Sample
  • Complex: Complex of RecA filament with homologous dsDNA containing 7-nt microhomology.
KeywordsRecombinase / DNA bound / D-loop / Homology search / DNA BINDING PROTEIN
Biological speciesE.Coli (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsMaeots ME / Enchev RI
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2059 United Kingdom
CitationJournal: biorxiv / Year: 2025
Title: Chronobot: Deep learning guided time-resolved cryo-EM captures molecular choreography of RecA in homology search
Authors: Maeots ME / Tupin S / Esfahani MMN / Molina JBR / Clapperton J / Amin A / Imbert A / Enchev RI
History
DepositionMay 28, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53921.png

Downloads & links

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Map

FileDownload / File: emd_53921.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus refinement of (RecAmini-filament dsDNA7-nt)250ms
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 512 pix.
= 486.4 Å		0.95 Å/pix.
x 512 pix.
= 486.4 Å		0.95 Å/pix.
x 512 pix.
= 486.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.03109396 - 0.061337885
Average (Standard dev.)0.000015444259 (±0.00054550066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 486.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3D class 1 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_1.map
Annotation3D class 1 of (RecAmini-filament dsDNA7-nt)250ms
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AxesZYX

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Additional map: 3D class 10 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_10.map
Annotation3D class 10 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 11 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_11.map
Annotation3D class 11 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 12 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_12.map
Annotation3D class 12 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 13 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_13.map
Annotation3D class 13 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 14 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_14.map
Annotation3D class 14 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 15 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_15.map
Annotation3D class 15 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 16 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_16.map
Annotation3D class 16 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 17 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_17.map
Annotation3D class 17 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 18 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_18.map
Annotation3D class 18 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 19 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_19.map
Annotation3D class 19 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 2 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_2.map
Annotation3D class 2 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 20 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_20.map
Annotation3D class 20 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 21 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_21.map
Annotation3D class 21 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 22 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_22.map
Annotation3D class 22 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 23 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_23.map
Annotation3D class 23 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 3 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_3.map
Annotation3D class 3 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 4 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_4.map
Annotation3D class 4 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 5 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_5.map
Annotation3D class 5 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 6 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_6.map
Annotation3D class 6 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 7 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_7.map
Annotation3D class 7 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 8 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_8.map
Annotation3D class 8 of (RecAmini-filament dsDNA7-nt)250ms
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Additional map: 3D class 9 of (RecAmini-filament dsDNA7-nt)250ms

Fileemd_53921_additional_9.map
Annotation3D class 9 of (RecAmini-filament dsDNA7-nt)250ms
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Half map: half-map 2 of consensus refinement

Fileemd_53921_half_map_1.map
Annotationhalf-map 2 of consensus refinement
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Half map: half-map 1 of consensus refinement

Fileemd_53921_half_map_2.map
Annotationhalf-map 1 of consensus refinement
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Sample components

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Entire : Complex of RecA filament with homologous dsDNA containing 7-nt mi...

EntireName: Complex of RecA filament with homologous dsDNA containing 7-nt microhomology.
Components
  • Complex: Complex of RecA filament with homologous dsDNA containing 7-nt microhomology.

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Supramolecule #1: Complex of RecA filament with homologous dsDNA containing 7-nt mi...

SupramoleculeName: Complex of RecA filament with homologous dsDNA containing 7-nt microhomology.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: E.Coli (others)
Molecular weightTheoretical: 500 KDa

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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

Concentration6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 28.5 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 700000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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