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- EMDB-7311: Structure of PRC2 bound to a H3K27me3/WT hetero-dinucleosome subs... -

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Basic information

Entry
Database: EMDB / ID: EMD-7311
TitleStructure of PRC2 bound to a H3K27me3/WT hetero-dinucleosome substrate with a 35 bp DNA linker. Masked refinement of PRC2-substrate nucleosome subcomplex.
Map dataStructure of human PRC2 bound to a hetero-dinucleosome substrate with 35 bp linker DNA. Refinement after signal subtraction of the modified nucleosome.
Sample
  • Complex: Structure of human PRC2 bound to a hetero-dinucleosome substrate with 35 bp linker DNA. Refinement after signal subtraction to increase resolution of the substrate nucleosome - PRC2 interface.
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 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: 0.039
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.039
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7311.png

Downloads & links

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Map

FileDownload / File: emd_7311.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of human PRC2 bound to a hetero-dinucleosome substrate with 35 bp linker DNA. Refinement after signal subtraction of the modified nucleosome.
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.039 / Movie #1: 0.039
Minimum - Maximum-0.032785326 - 0.11663936
Average (Standard dev.)-2.0933183e-05 (±0.0033617574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 475.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z475.200475.200475.200
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/NS360360360
D min/max/mean-0.0330.117-0.000

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Supplemental data

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Sample components

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

EntireName: Structure of human PRC2 bound to a hetero-dinucleosome substrate with 35 bp linker DNA. Refinement after signal subtraction to increase resolution of the substrate nucleosome - PRC2 interface.
Components
  • Complex: Structure of human PRC2 bound to a hetero-dinucleosome substrate with 35 bp linker DNA. Refinement after signal subtraction to increase resolution of the substrate nucleosome - PRC2 interface.

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Supramolecule #1: Structure of human PRC2 bound to a hetero-dinucleosome substrate ...

SupramoleculeName: Structure of human PRC2 bound to a hetero-dinucleosome substrate with 35 bp linker DNA. Refinement after signal subtraction to increase resolution of the substrate nucleosome - PRC2 interface.
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Signal subtraction of the particle images was performed to exclude signal from the more flexible modified nucleosome from the reconstruction.
Number images used: 93384
FSC plot (resolution estimation)

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