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- EMDB-8062: Cryo-EM structure of Nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-8062
TitleCryo-EM structure of Nucleosome
Map dataNone
Sample
  • Complex: Nucleosome core particle
Biological speciesXenopus (frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsHalic M / Zocco M
CitationJournal: Cell Discov / Year: 2016
Title: The Chp1 chromodomain binds the H3K9me tail and the nucleosome core to assemble heterochromatin.
Authors: Manuel Zocco / Mirela Marasovic / Paola Pisacane / Silvija Bilokapic / Mario Halic /
Abstract: To maintain genome stability, cells pack large portions of their genome into silent chromatin or heterochromatin. Histone H3 lysine 9 methylation, a hallmark of heterochromatin, is recognized by ...To maintain genome stability, cells pack large portions of their genome into silent chromatin or heterochromatin. Histone H3 lysine 9 methylation, a hallmark of heterochromatin, is recognized by conserved readers called chromodomains. But how chromodomains interact with their actual binding partner, the H3K9 methylated nucleosome, remains elusive. We have determined the structure of a nucleosome trimethylated at lysine 9 of histone H3 (H3K9me3 Nucleosome) in a complex with the chromodomain of Chp1, a protein required for RNA interference-dependent heterochromatin formation in fission yeast. The cryo-electron microscopy structure reveals that the chromodomain of Chp1 binds the histone H3 lysine 9 methylated tail and the core of the nucleosome, primarily histones H3 and H2B. Mutations in chromodomain of Chp1 loops, which interact with the nucleosome core, abolished this interaction in vitro. Moreover, fission yeast cells with Chp1 loop mutations have a defect in Chp1 recruitment and heterochromatin formation. This study reveals the structural basis for heterochromatic silencing and suggests that chromodomains could read histone code in the H3 tail and the nucleosome core, which would provide an additional layer of regulation.
History
DepositionJan 25, 2016-
Header (metadata) releaseAug 10, 2016-
Map releaseAug 10, 2016-
UpdateJul 26, 2017-
Current statusJul 26, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8062.png

Downloads & links

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Map

FileDownload / File: emd_8062.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.9 Å/pix.
x 100 pix.
= 190. Å		1.9 Å/pix.
x 100 pix.
= 190. Å		1.9 Å/pix.
x 100 pix.
= 190. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.08832989 - 0.17097336
Average (Standard dev.)0.00065142993 (±0.014914555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 190.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.91.91.9
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z190.000190.000190.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0880.1710.001

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Supplemental data

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Sample components

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Entire : Nucleosome core particle

EntireName: Nucleosome core particle
Components
  • Complex: Nucleosome core particle

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Supramolecule #1: Nucleosome core particle

SupramoleculeName: Nucleosome core particle / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus (frog)
Recombinant expressionOrganism: Enterobacteria phage L1 (virus) / Recombinant plasmid: pBRww2
Molecular weightTheoretical: 170 KDa

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 25000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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