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- EMDB-9694: The complete structure of yeast COMPASS -

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Basic information

Entry
Database: EMDB / ID: EMD-9694
TitleThe complete structure of yeast COMPASS
Map datathe complete yeast COMPASS complex
Sample
  • Complex: COMPASS
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsWang YX / Ding ZY
CitationJournal: Sci Rep / Year: 2018
Title: Architecture and subunit arrangement of the complete Saccharomyces cerevisiae COMPASS complex.
Authors: Yanxing Wang / Zhanyu Ding / Xiangyang Liu / Yu Bao / Min Huang / Catherine C L Wong / Xiaoyu Hong / Yao Cong /
Abstract: Methylation of histone H3 lysine 4 (H3K4) is catalyzed by the multi-component COMPASS or COMPASS-like complex, which is highly conserved from yeast to human, and plays essential roles in gene ...Methylation of histone H3 lysine 4 (H3K4) is catalyzed by the multi-component COMPASS or COMPASS-like complex, which is highly conserved from yeast to human, and plays essential roles in gene expression and transcription, cell cycle progression, and DNA repair. Here we present a cryo-EM map of the complete S. cerevisiae COMPASS complex. Through tag or Fab labeling strategy combined with cryo-EM 3D reconstruction and cross-linking and mass spectrometry (XL-MS) analysis, we uncovered new information on the subunit arrangement: Cps50, Cps35, and Cps30 were determined to group together to form the face region in the head of the complex, and Cps40 and the N-terminal portion of Set1 reside on the top of the head. Our map reveals the location of the active center and a canyon in the back of the head. Together, our study provides the first snapshot of the complete architecture of yeast COMPASS and a picture of its subunit interaction network, which could facilitate our understanding of the COMPASS machinery and its functionality.
History
DepositionOct 23, 2018-
Header (metadata) releaseDec 12, 2018-
Map releaseDec 12, 2018-
UpdateDec 12, 2018-
Current statusDec 12, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.928
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.928
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9694.png

Downloads & links

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Map

FileDownload / File: emd_9694.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe complete yeast COMPASS complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 220 pix.
= 290.4 Å		1.32 Å/pix.
x 220 pix.
= 290.4 Å		1.32 Å/pix.
x 220 pix.
= 290.4 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: 0.928 / Movie #1: 0.928
Minimum - Maximum-0.5513563 - 1.5108188
Average (Standard dev.)0.0195028 (±0.12369563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-110-110-110
Dimensions220220220
Spacing220220220
CellA=B=C: 290.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z290.400290.400290.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS-110-110-110
NC/NR/NS220220220
D min/max/mean-0.5511.5110.020

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Supplemental data

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Sample components

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Entire : COMPASS

EntireName: COMPASS
Components
  • Complex: COMPASS

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Supramolecule #1: COMPASS

SupramoleculeName: COMPASS / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77865
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION

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