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- EMDB-7310: Structure of human PRC2 bound to a hetero-dinucleosome substrate ... -

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Basic information

Entry
Database: EMDB / ID: 7310
TitleStructure of human PRC2 bound to a hetero-dinucleosome substrate with 35 bp linker DNA. 3D classification of signal subtracted particles lacking the unmodified substrate nucleosome. Example Class3.
Map dataStructure of human PRC2 bound to a hetero-dinucleosome substrate with 35 bp linker DNA. 3D classification of signal subtracted particles lacking the unmodified substrate nucleosome. Example Class3.
SampleHuman Polycomb Repressive Complex 2 (PRC2) in complex with a heterodinucleosome composed of an unmodified nucleosome and a nucleosome carrying an H3K27 pseudo-trimethyl mark with 35 bp. Subclassification of the overall reconstruction after signal subtraction. Example Class3.:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 10.1 Å resolution
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
DateDeposition: Dec 20, 2017 / Header (metadata) release: Jan 31, 2018 / Map release: Jan 31, 2018 / Last update: Jan 31, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7310.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.32 Å/pix.
= 475.2 Å
360 pix
1.32 Å/pix.
= 475.2 Å
360 pix
1.32 Å/pix.
= 475.2 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
Contour Level:0.025 (by author), 0.025 (movie #1):
Minimum - Maximum-0.021511182 - 0.08791673
Average (Standard dev.)0.0000020907564 (0.0031695024)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 475.2 Å
α=β=γ: 90.0 deg.

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/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0220.0880.000

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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 with 35 bp. Subclassification of the overall reconstruction after signal subtraction. Example Class3.
Number of components: 1

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Component #1: protein, Human Polycomb Repressive Complex 2 (PRC2) in complex wi...

ProteinName: 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 with 35 bp. Subclassification of the overall reconstruction after signal subtraction. Example Class3.
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 15104
3D reconstructionResolution: 10.1 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Overall reconstruction was subjected to signal subtraction procedure to allow 3D subclassification of the part of the complex including the modified nucleosome.
FSC plot
(resolution estimation)

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