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- EMDB-56612: Structure of the human inner kinetochore CCAN bound to a di-CENP-... -

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Basic information

Entry
Database: EMDB / ID: EMD-56612
TitleStructure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome, consensus map
Map data
Sample
  • Complex: Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome
KeywordsCentromeres / Kinetochores / CELL CYCLE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.9 Å
AuthorsYu C / Barford D
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_120 United Kingdom
Cancer Research UKC576/A25675 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Models for the architecture of the human inner kinetochore on centromeric α-satellite CENP-A nucleosome arrays.
Authors: Cong Yu / Kyle W Muir / Jing Yang / Ziguo Zhang / Stephen H McLaughlin / David Barford /
Abstract: Human kinetochores assemble onto centromeric DNA comprising repetitive arrays of the 171 bp α-satellite sequence. To understand the higher-order architecture of the inner kinetochore assembled ...Human kinetochores assemble onto centromeric DNA comprising repetitive arrays of the 171 bp α-satellite sequence. To understand the higher-order architecture of the inner kinetochore assembled onto α-satellite arrays, we show cryo-EM structures of CCAN with free DNA, and α-satellite repeat monomers and dimers with CENP-A nucleosomes. CCAN bound to free DNA and a monomeric CENP-A nucleosome engages 70 bp of DNA comprising 30 bp of an upstream α-satellite repeat. This upstream DNA interacts with the histone-fold domain subunits of the CENP-TWSX module in a manner resembling how nucleosomes wrap DNA gyres. A complex of CCAN assembled onto a dimeric α-satellite repeat with two CENP-A nucleosomes shows that CCAN can only be accommodated on the linker DNA by unwrapping DNA from both the CENP-TWSX module and the upstream nucleosome. We discuss the implications of these results for models of CCAN assembly on arrays of α-satellite chromatin containing CENP-A nucleosomes.
History
DepositionFeb 9, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56612.png

Downloads & links

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Map

FileDownload / File: emd_56612.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 371.2 Å		0.93 Å/pix.
x 400 pix.
= 371.2 Å		0.93 Å/pix.
x 400 pix.
= 371.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.928 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0009
Minimum - Maximum-0.0013337575 - 0.005712923
Average (Standard dev.)0.00002937882 (±0.00038576598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 371.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56612_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_56612_half_map_2.map
Projections & Slices
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Sample components

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Entire : Structure of the human inner kinetochore CCAN bound to a di-CENP-...

EntireName: Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome
Components
  • Complex: Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome

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Supramolecule #1: Structure of the human inner kinetochore CCAN bound to a di-CENP-...

SupramoleculeName: Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18, #22
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: 10.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 15057
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial modelPDB ID:

7r5s


Chain - Source name: PDB / Chain - Initial model type: experimental model

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