[English] 日本語
Yorodumi
- EMDB-7306: Structure of PRC2 bound to a H3K27me3/WT hetero-dinucleosome subs... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7306
TitleStructure of PRC2 bound to a H3K27me3/WT hetero-dinucleosome substrate with a 35 bp DNA linker
Map dataComplete Map of the PRC2 catalyitic lobe bound to a hetero-dinucleosome
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
    • Protein or peptide: EZH2
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7306.png

Downloads & links

-
Map

FileDownload / File: emd_7306.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplete Map of the PRC2 catalyitic lobe bound to a hetero-dinucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 360 pix.
= 475.2 Å		1.32 Å/pix.
x 360 pix.
= 475.2 Å		1.32 Å/pix.
x 360 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.028158827 - 0.11287831
Average (Standard dev.)8.9167326e-05 (±0.0035840597)
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-0.0280.1130.000

-
Supplemental data

-
Half map: half map 1

Fileemd_7306_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_7306_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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
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
    • Protein or peptide: EZH2

-
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
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

-
Macromolecule #1: EZH2

MacromoleculeName: EZH2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MGQTGKKSEK GPVCWRKRVK SEYMRLRQLK RFRRADEVKS MFSSNRQKIL ERTEILNQEW KQRRIQPVH ILTSVSSLRG TRECSVTSDL DFPTQVIPLK TLNAVASVPI MYSWSPLQQN F MVEDETVL HNIPYMGDEV LDQDGTFIEE LIKNYDGKVH GDRECGFIND ...String:
MGQTGKKSEK GPVCWRKRVK SEYMRLRQLK RFRRADEVKS MFSSNRQKIL ERTEILNQEW KQRRIQPVH ILTSVSSLRG TRECSVTSDL DFPTQVIPLK TLNAVASVPI MYSWSPLQQN F MVEDETVL HNIPYMGDEV LDQDGTFIEE LIKNYDGKVH GDRECGFIND EIFVELVNAL GQ YNDDDDD DDGDDPEERE EKQKDLEDHR DDKESRPPRK FPSDKIFEAI SSMFPDKGTA EEL KEKYKE LTEQQLPGAL PPECTPNIDG PNAKSVQREQ SLHSFHTLFC RRCFKYDCFL HPFH ATPNT YKRKNTETAL DNKPCGPQCY QHLEGAKEFA AALTAERIKT PPKRPGGRRR GRLPN NSSR PSTPTINVLE SKDTDSDREA GTETGGENND KEEEEKKDET SSSSEANSRC QTPIKM KPN IEPPENVEWS GAEASMFRVL IGTYYDNFCA IARLIGTKTC RQVYEFRVKE SSIIAPA PA EDVDTPPRKK KRKHRLWAAH CRKIQLKKDG SSNHVYNYQP CDHPRQPCDS SCPCVIAQ N FCEKFCQCSS ECQNRFPGCR CKAQCNTKQC PCYLAVRECD PDLCLTCGAA DHWDSKNVS CKNCSIQRGS KKHLLLAPSD VAGWGIFIKD PVQKNEFISE YCGEIISQDE ADRRGKVYDK YMCSFLFNL NNDFVVDATR KGNKIRFANH SVNPNCYAKV MMVNGDHRIG IFAKRAIQTG E ELFFDYRY SQADALKYVG IEREMEIP

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.9
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Number real images: 4600 / Average exposure time: 8.7 sec. / 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

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93384
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more