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- EMDB-72232: Local refinement of CX3 body of BCDX2-CX3-RAD51 complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-72232
TitleLocal refinement of CX3 body of BCDX2-CX3-RAD51 complex
Map dataLocal refinement of CX3 body of BCDX2-CX3-RAD51 complex, unsharpened
Sample
  • Complex: DX2-CX3-RAD51 filament
KeywordsRAD51 paralog / DX2-CX3 complex / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsKoo CW / Ciferri C / Yatskevich S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Tumor suppressors BCDX2-CX3 supercomplex and DX2-CX3 complex template RAD51 filament formation
Authors: Koo CW / Ciferri C / Yatskevich S
History
DepositionAug 20, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72232.png

Downloads & links

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Map

FileDownload / File: emd_72232.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement of CX3 body of BCDX2-CX3-RAD51 complex, unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 373.6 Å		0.93 Å/pix.
x 400 pix.
= 373.6 Å		0.93 Å/pix.
x 400 pix.
= 373.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.934 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0426
Minimum - Maximum-0.15310486 - 0.4237623
Average (Standard dev.)0.00016881536 (±0.0056187394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 373.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local refinement of CX3 body of BCDX2-CX3-RAD51 complex, sharpened

Fileemd_72232_additional_1.map
AnnotationLocal refinement of CX3 body of BCDX2-CX3-RAD51 complex, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local refinement of CX3 body of BCDX2-CX3-RAD51 complex, half-map A

Fileemd_72232_half_map_1.map
AnnotationLocal refinement of CX3 body of BCDX2-CX3-RAD51 complex, half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local refinement of CX3 body of BCDX2-CX3-RAD51 complex, half-map B

Fileemd_72232_half_map_2.map
AnnotationLocal refinement of CX3 body of BCDX2-CX3-RAD51 complex, half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DX2-CX3-RAD51 filament

EntireName: DX2-CX3-RAD51 filament
Components
  • Complex: DX2-CX3-RAD51 filament

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Supramolecule #1: DX2-CX3-RAD51 filament

SupramoleculeName: DX2-CX3-RAD51 filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 12.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 131263
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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