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- EMDB-7312: Structure of human PRC2 bound to a hetero-dinucleosome substrate ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7312
TitleStructure of human PRC2 bound to a hetero-dinucleosome substrate with 35 bp linker DNA. Refinement after signal subtraction of the modified nucleosome ton improve resolution of the substrate nucleosome - PRC2 interface.
Map dataStructure of human PRC2 bound to a hetero-dinucleosome substrate with 30 bp linker DNA. Refinement after signal subtraction of the modified nucleosome.
Sample
  • Complex: Human Polycomb Repressive Complex 2 (PRC2) in complex with a heterodinucleosome composed of an unmodified nucleosome and a nucleosome carrying an H3K27 pseudo-trimethyl mark, connected by 30 bp of linker DNA
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsPoepsel S / Kasinath V / Nogales E
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes.
Authors: Simon Poepsel / Vignesh Kasinath / Eva Nogales /
Abstract: Epigenetic regulation is mediated by protein complexes that couple recognition of chromatin marks to activity or recruitment of chromatin-modifying enzymes. Polycomb repressive complex 2 (PRC2), a ...Epigenetic regulation is mediated by protein complexes that couple recognition of chromatin marks to activity or recruitment of chromatin-modifying enzymes. Polycomb repressive complex 2 (PRC2), a gene silencer that methylates lysine 27 of histone H3, is stimulated upon recognition of its own catalytic product and has been shown to be more active on dinucleosomes than H3 tails or single nucleosomes. These properties probably facilitate local H3K27me2/3 spreading, causing heterochromatin formation and gene repression. Here, cryo-EM reconstructions of human PRC2 bound to bifunctional dinucleosomes show how a single PRC2, via interactions with nucleosomal DNA, positions the H3 tails of the activating and substrate nucleosome to interact with the EED subunit and the SET domain of EZH2, respectively. We show how the geometry of the PRC2-DNA interactions allows PRC2 to accommodate varying lengths of the linker DNA between nucleosomes. Our structures illustrate how an epigenetic regulator engages with a complex chromatin substrate.
History
DepositionDec 20, 2017-
Header (metadata) releaseJan 31, 2018-
Map releaseJan 31, 2018-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.031
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.031
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7312.png

Downloads & links

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Map

FileDownload / File: emd_7312.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of human PRC2 bound to a hetero-dinucleosome substrate with 30 bp linker DNA. Refinement after signal subtraction of the modified nucleosome.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.031 / Movie #1: 0.031
Minimum - Maximum-0.02478971 - 0.112097874
Average (Standard dev.)0.00012808538 (±0.004145158)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0250.1120.000

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Supplemental data

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Sample components

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Entire : Human Polycomb Repressive Complex 2 (PRC2) in complex with a hete...

EntireName: Human Polycomb Repressive Complex 2 (PRC2) in complex with a heterodinucleosome composed of an unmodified nucleosome and a nucleosome carrying an H3K27 pseudo-trimethyl mark, connected by 30 bp of linker DNA
Components
  • Complex: Human Polycomb Repressive Complex 2 (PRC2) in complex with a heterodinucleosome composed of an unmodified nucleosome and a nucleosome carrying an H3K27 pseudo-trimethyl mark, connected by 30 bp of linker DNA

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Supramolecule #1: Human Polycomb Repressive Complex 2 (PRC2) in complex with a hete...

SupramoleculeName: Human Polycomb Repressive Complex 2 (PRC2) in complex with a heterodinucleosome composed of an unmodified nucleosome and a nucleosome carrying an H3K27 pseudo-trimethyl mark, connected by 30 bp of linker DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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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: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Signal subtraction was employed to remove the signal from the more flexible modified nucleosome from the particle images.
Number images used: 27182
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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