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- EMDB-77485: Local multi-body refinement of bmCCAN-1, part of the dimeric bmCC... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-77485
TitleLocal multi-body refinement of bmCCAN-1, part of the dimeric bmCCAN-DNA complex
Map dataCCAN-1 body of the bmCCAN-DNA dimer multi body refinement
Sample
  • Complex: Bombyx mori CCAN dimer bound to DNA
KeywordsCCAN / complex / protein-DNA / segregation / DNA BINDING PROTEIN
Biological speciesBombyx mori (domestic silkworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsYatskevich S / Ciferri C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Architecture and Function of Holocentric CENP-A-Independent Inner Kinetochores
Authors: Yatskevich S / Ciferri C
History
DepositionJun 5, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77485.png

Downloads & links

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Map

FileDownload / File: emd_77485.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCCAN-1 body of the bmCCAN-DNA dimer multi body refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 400 pix.
= 435. Å		1.09 Å/pix.
x 400 pix.
= 435. Å		1.09 Å/pix.
x 400 pix.
= 435. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0875 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00305
Minimum - Maximum-0.008510282 - 0.019007616
Average (Standard dev.)-0.0000105754325 (±0.00058656355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 435.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CCAN-1 body of the bmCCAN-DNA dimer multi body refinement, sharpened

Fileemd_77485_additional_1.map
AnnotationCCAN-1 body of the bmCCAN-DNA dimer multi body refinement, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77485_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77485_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 : Bombyx mori CCAN dimer bound to DNA

EntireName: Bombyx mori CCAN dimer bound to DNA
Components
  • Complex: Bombyx mori CCAN dimer bound to DNA

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Supramolecule #1: Bombyx mori CCAN dimer bound to DNA

SupramoleculeName: Bombyx mori CCAN dimer bound to DNA / type: complex / ID: 1 / Parent: 0
Macromolecule list: #5, #8, #6-#7, #9-#13, #1, #3-#4, #2, #14-#15
Source (natural)Organism: Bombyx mori (domestic silkworm)

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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

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.5 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: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 23990
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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