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- EMDB-26333: Cryo-EM structure of centromeric chromatin array shaped by the ki... -

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Basic information

Entry
Database: EMDB / ID: EMD-26333
TitleCryo-EM structure of centromeric chromatin array shaped by the kinetochore protein CENP-N
Map data
Sample
  • Complex: Centromeric chromatin array in complex with kinetochore protein CENP-N
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsZhou K / Luger K
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: CENP-N promotes the compaction of centromeric chromatin.
Authors: Keda Zhou / Magdalena Gebala / Dustin Woods / Kousik Sundararajan / Garrett Edwards / Dan Krzizike / Jeff Wereszczynski / Aaron F Straight / Karolin Luger /
Abstract: The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How ...The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How nucleosomes at the centromere arrange into higher order structures is unknown. Here we demonstrate that the human CENP-A-interacting protein CENP-N promotes the stacking of CENP-A-containing mononucleosomes and nucleosomal arrays through a previously undefined interaction between the α6 helix of CENP-N with the DNA of a neighboring nucleosome. We describe the cryo-EM structures and biophysical characterization of such CENP-N-mediated nucleosome stacks and nucleosomal arrays and demonstrate that this interaction is responsible for the formation of densely packed chromatin at the centromere in the cell. Our results provide first evidence that CENP-A, together with CENP-N, promotes specific chromatin higher order structure at the centromere.
History
DepositionFeb 28, 2022-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateJun 15, 2022-
Current statusJun 15, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26333.png

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Map

FileDownload / File: emd_26333.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.48 Å/pix.
x 256 pix.
= 634.88 Å		2.48 Å/pix.
x 256 pix.
= 634.88 Å		2.48 Å/pix.
x 256 pix.
= 634.88 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.48 Å
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Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.49257267 - 1.5480273
Average (Standard dev.)0.0052414024 (±0.081314474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 634.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26333_msk_1.map
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Half map: #1

Fileemd_26333_half_map_1.map
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Half map: #2

Fileemd_26333_half_map_2.map
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Sample components

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Entire : Centromeric chromatin array in complex with kinetochore protein CENP-N

EntireName: Centromeric chromatin array in complex with kinetochore protein CENP-N
Components
  • Complex: Centromeric chromatin array in complex with kinetochore protein CENP-N

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Supramolecule #1: Centromeric chromatin array in complex with kinetochore protein CENP-N

SupramoleculeName: Centromeric chromatin array in complex with kinetochore protein CENP-N
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 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: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9305
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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