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- EMDB-2693: MAPPING THE DEUBIQUITINATION MODULE WITHIN THE SAGA COMPLEX -

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Basic information

Entry
Database: EMDB / ID: EMD-2693
TitleMAPPING THE DEUBIQUITINATION MODULE WITHIN THE SAGA COMPLEX
Map dataStructure of the yeast (S. cerevisiae) SAGA complex
Sample
  • Sample: S. cerevisiae SAGA complex
  • Protein or peptide: SAGA
KeywordsSAGA / Eukaryotic Transcription / Deubiquitination module
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 30.3 Å
AuthorsDurand A / Bonnet J / Fournier M / Schultz P
CitationJournal: Structure / Year: 2014
Title: Mapping the deubiquitination module within the SAGA complex.
Abstract: The molecular organization of the yeast transcriptional coactivator Spt-Ada-Gcn5 acetyltransferase (SAGA) was analyzed by single-particle electron microscopy. Complete or partial deletion of the ...The molecular organization of the yeast transcriptional coactivator Spt-Ada-Gcn5 acetyltransferase (SAGA) was analyzed by single-particle electron microscopy. Complete or partial deletion of the Sgf73 subunit disconnects the deubiquitination (DUB) module from SAGA and favors in our conditions the cleavage of the C-terminal ends of the Spt7 subunit and the loss of the Spt8 subunit. The structural comparison of the wild-type SAGA with two deletion mutants positioned the DUB module and enabled the fitting of the available atomic models. The localization of the DUB module close to Gcn5 defines a chromatin-binding interface within SAGA, which could be demonstrated by the binding of nucleosome core particles. The TATA-box binding protein (TBP)-interacting subunit Spt8 was found to be located close to the DUB but in a different domain than Spt3, also known to contact TBP. A flexible protein arm brings both subunits close enough to interact simultaneously with TBP.
History
DepositionJun 26, 2014-
Header (metadata) releaseJul 23, 2014-
Map releaseDec 10, 2014-
UpdateDec 10, 2014-
Current statusDec 10, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2693-126...

Downloads & links

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Map

FileDownload / File: emd_2693.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the yeast (S. cerevisiae) SAGA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 192 pix.
= 510.72 Å		2.66 Å/pix.
x 192 pix.
= 510.72 Å		2.66 Å/pix.
x 192 pix.
= 510.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-7.18650293 - 14.40225601
Average (Standard dev.)0.08276498 (±0.80129594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 510.72003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.662.662.66
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z510.720510.720510.720
α/β/γ90.00090.00090.000
start NX/NY/NZ-180-180-179
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-7.18714.4020.083

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Supplemental data

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Sample components

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Entire : S. cerevisiae SAGA complex

EntireName: S. cerevisiae SAGA complex
Components
  • Sample: S. cerevisiae SAGA complex
  • Protein or peptide: SAGA

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Supramolecule #1000: S. cerevisiae SAGA complex

SupramoleculeName: S. cerevisiae SAGA complex / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 1
Molecular weightTheoretical: 1.8 MDa

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Macromolecule #1: SAGA

MacromoleculeName: SAGA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4742 / synonym: Baker's yeast / Location in cell: Nuclear
Molecular weightTheoretical: 1.8 MDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8 / Details: 500 mM NaCl, 30 mM Hepes, 2 mM EGTA
StainingType: NEGATIVE
Details: Grids with adsorbed protein stained with 2% w/v uranyl acetate
GridDetails: 300 mesh Cu/Rh grid with glow discharge
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateOct 10, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 53846 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsIMAGIC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.3 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 19226
Final two d classificationNumber classes: 500

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