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- EMDB-77477: apo-bmCCAN consensus refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-77477
Titleapo-bmCCAN consensus refinement
Map dataConsensus apo-bmCCAN refinement
Sample
  • Complex: Bombyx mori apo-CCAN
KeywordsCCAN / complex / protein-DNA / segregation / DNA BINDING PROTEIN
Biological speciesBombyx mori (domestic silkworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsYatskevich S / Ciferri C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2026
Title: Architecture and function of holocentric CENP-A-independent inner kinetochores.
Authors: Christine Yu / Sundar Ram Sankaranarayanan / Gaetan Cornilleau / Anna C Howes / Caleigh M Azumaya / Eric S Day / Inna Zilberleyb / Bobby Brillantes / Tommy K Cheung / Leonie Dec / Damarys ...Authors: Christine Yu / Sundar Ram Sankaranarayanan / Gaetan Cornilleau / Anna C Howes / Caleigh M Azumaya / Eric S Day / Inna Zilberleyb / Bobby Brillantes / Tommy K Cheung / Leonie Dec / Damarys Loew / Phong Tran / Christopher M Rose / Ines Anna Drinnenberg / Claudio Ciferri / Stanislau Yatskevich /
Abstract: Kinetochores are essential macromolecular complexes anchoring chromosomes to the mitotic spindle, ensuring faithful cell division. Despite their critical role, the structural organization of ...Kinetochores are essential macromolecular complexes anchoring chromosomes to the mitotic spindle, ensuring faithful cell division. Despite their critical role, the structural organization of kinetochores across diverse species remains poorly understood. We present the inner kinetochore constitutive centromere-associated network (CCAN) structure of the silkmoth , an insect that lacks the canonical centromere-specifying histone variant CENP-A and exhibits chromosome-wide centromeric activity (holocentric). The CCAN incorporates four previously uncharacterized centromeric subunit proteins that are structurally related to the Dam1/DASH complex but function in scaffolding the inner kinetochore rather than in microtubule binding. Similar to the yeast and human systems, the CCAN also entraps DNA within its central closed chamber. However, unlike these systems, the CCAN can also assemble in vitro into a self-contained head-to-head dimer via atypical histone-fold protein dimerization. On the basis of our findings, we propose that the holocentric organization may emerge from the modular arrangement of discrete kinetochore units.
History
DepositionJun 5, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77477.png

Downloads & links

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Map

FileDownload / File: emd_77477.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus apo-bmCCAN refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 335.2 Å		0.84 Å/pix.
x 400 pix.
= 335.2 Å		0.84 Å/pix.
x 400 pix.
= 335.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.838 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0389
Minimum - Maximum-0.22963305 - 0.42431462
Average (Standard dev.)-0.00006594935 (±0.0074737053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 335.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Consensus apo-bmCCAN refinement, unsharpened

Fileemd_77477_additional_1.map
AnnotationConsensus apo-bmCCAN refinement, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77477_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_77477_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 apo-CCAN

EntireName: Bombyx mori apo-CCAN
Components
  • Complex: Bombyx mori apo-CCAN

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Supramolecule #1: Bombyx mori apo-CCAN

SupramoleculeName: Bombyx mori apo-CCAN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
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: 62.0 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: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 265941
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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