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- EMDB-10158: Class 1B : CENP-A nucleosome -

Open data

ID or keywords:


Basic information

Database: EMDB / ID: EMD-10158
TitleClass 1B : CENP-A nucleosome
Map data
SampleClass 1B : CENP-A nucleosome
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsAli-Ahmad A / Bilokapic S / Halic M / Sekulic N
Funding support Norway, Germany, 2 items
OrganizationGrant numberCountry
Norwegian Research Council263195 Norway
European Research CouncilERC-smallRNAhet-309584 Germany
CitationJournal: EMBO Rep. / Year: 2019
Title: CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail.
Authors: Ahmad Ali-Ahmad / Silvija Bilokapić / Ingmar B Schäfer / Mario Halić / Nikolina Sekulić /
Abstract: Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is ...Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is considered to be a central organizer of the CCAN. We provide new molecular insights into the structure of human CENP-A nucleosomes, in isolation and in complex with the CENP-C central region (CENP-C ), the main CENP-A binding module of human CENP-C. We establish that the short αN helix of CENP-A promotes DNA flexibility at the nucleosome ends, independently of the sequence it wraps. Furthermore, we show that, in vitro, two regions of human CENP-C (CENP-C and CENP-C ) both bind exclusively to the CENP-A nucleosome. We find CENP-C to bind with high affinity due to an extended hydrophobic area made up of CENP-A and CENP-A . Importantly, we identify two key conformational changes within the CENP-A nucleosome upon CENP-C binding. First, the loose DNA wrapping of CENP-A nucleosomes is further exacerbated, through destabilization of the H2A C-terminal tail. Second, CENP-C rigidifies the N-terminal tail of H4 in the conformation favoring H4 monomethylation, essential for a functional centromere.
DepositionJul 30, 2019-
Header (metadata) releaseAug 14, 2019-
Map releaseAug 14, 2019-
UpdateOct 16, 2019-
Current statusOct 16, 2019Processing site: PDBe / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0094
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0094
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_10158.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å
1.06 Å/pix.
x 240 pix.
= 254.4 Å
1.06 Å/pix.
x 240 pix.
= 254.4 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Contour LevelBy AUTHOR: 0.0094 / Movie #1: 0.0094
Minimum - Maximum-0.011242212 - 0.038722683
Average (Standard dev.)0.00025123052 (±0.002015702)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z254.400254.400254.400
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0110.0390.000

Supplemental data

Sample components

Entire Class 1B : CENP-A nucleosome

EntireName: Class 1B : CENP-A nucleosome / Number of components: 1

Component #1: protein, Class 1B : CENP-A nucleosome

ProteinName: Class 1B : CENP-A nucleosome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.2 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 47000
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF

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