[English] 日本語
Yorodumi
- EMDB-6301: S. cerevisiae SAGA complex in the donut conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6301
TitleS. cerevisiae SAGA complex in the donut conformation
Map data3D reconstruction of the donut conformation of SAGA
Sample
  • Sample: The donut conformation of the yeast SAGA complex
  • Protein or peptide: Spt-Ada-Gcn5 Acetyltransferase Complex
KeywordsHistone acetyltransferase
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 38.9 Å
AuthorsSetiaputra D / Ross JD / Lu S / Cheng DT / Dong MQ / Yip CK
CitationJournal: J Biol Chem / Year: 2015
Title: Conformational flexibility and subunit arrangement of the modular yeast Spt-Ada-Gcn5 acetyltransferase complex.
Authors: Dheva Setiaputra / James D Ross / Shan Lu / Derrick T Cheng / Meng-Qiu Dong / Calvin K Yip /
Abstract: The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex is a highly conserved, 19-subunit histone acetyltransferase complex that activates transcription through acetylation and deubiquitination of ...The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex is a highly conserved, 19-subunit histone acetyltransferase complex that activates transcription through acetylation and deubiquitination of nucleosomal histones in Saccharomyces cerevisiae. Because SAGA has been shown to display conformational variability, we applied gradient fixation to stabilize purified SAGA and systematically analyzed this flexibility using single-particle EM. Our two- and three-dimensional studies show that SAGA adopts three major conformations, and mutations of specific subunits affect the distribution among these. We also located the four functional modules of SAGA using electron microscopy-based labeling and transcriptional activator binding analyses and show that the acetyltransferase module is localized in the most mobile region of the complex. We further comprehensively mapped the subunit interconnectivity of SAGA using cross-linking mass spectrometry, revealing that the Spt and Taf subunits form the structural core of the complex. These results provide the necessary restraints for us to generate a model of the spatial arrangement of all SAGA subunits. According to this model, the chromatin-binding domains of SAGA are all clustered in one face of the complex that is highly flexible. Our results relate information of overall SAGA structure with detailed subunit level interactions, improving our understanding of its architecture and flexibility.
History
DepositionMar 11, 2015-
Header (metadata) releaseMay 27, 2015-
Map releaseJun 3, 2015-
UpdateJun 3, 2015-
Current statusJun 3, 2015Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.239
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.239
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6301.gif

Downloads & links

-
Map

FileDownload / File: emd_6301.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of the donut conformation of SAGA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.67 Å/pix.
x 128 pix.
= 597.76 Å		4.67 Å/pix.
x 128 pix.
= 597.76 Å		4.67 Å/pix.
x 128 pix.
= 597.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.239 / Movie #1: 0.239
Minimum - Maximum-0.0214361 - 0.92349243
Average (Standard dev.)0.00635893 (±0.05065207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 597.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.674.674.67
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z597.760597.760597.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0210.9230.006

-
Supplemental data

-
Sample components

-
Entire : The donut conformation of the yeast SAGA complex

EntireName: The donut conformation of the yeast SAGA complex
Components
  • Sample: The donut conformation of the yeast SAGA complex
  • Protein or peptide: Spt-Ada-Gcn5 Acetyltransferase Complex

-
Supramolecule #1000: The donut conformation of the yeast SAGA complex

SupramoleculeName: The donut conformation of the yeast SAGA complex / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 1.7 MDa

-
Macromolecule #1: Spt-Ada-Gcn5 Acetyltransferase Complex

MacromoleculeName: Spt-Ada-Gcn5 Acetyltransferase Complex / type: protein_or_peptide / ID: 1 / Name.synonym: SAGA
Details: Samples were prepared using gradient fixation using a glycerol gradient and glutaraldehyde.
Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: SF1 / synonym: Yeast / Location in cell: Nucleus
Molecular weightTheoretical: 1.7 MDa

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Details: 40 mM HEPES, 150 mM NaCl, 20% glycerol, 0.1% Tween-20, 0.015% glutaraldehyde
StainingType: NEGATIVE
Details: Grids with adsorbed protein were used to scoop a carbon layer floating on 0.75% w/v uranyl formate, sandwiching the protein and a layer of stain between two carbon layers.
GridDetails: 400 mesh copper grid with holey carbon support, glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
TemperatureAverage: 298 K
DetailsLow dose
DateFeb 10, 2013
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 1.3 µm / Number real images: 382 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 65900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 49000
Sample stageSpecimen holder: Side entry room temperature tomography holder
Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -65
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

-
Image processing

DetailsParticles were selected manually.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 38.9 Å / Resolution method: OTHER / Software - Name: Spider
Details: The initial map was made using back-projection of tilted data, and was subjected to an angular refinement cycle with the same data set. The model then underwent a final refinement cycle with ...Details: The initial map was made using back-projection of tilted data, and was subjected to an angular refinement cycle with the same data set. The model then underwent a final refinement cycle with both tilted and untilted data. The model was then filtered to the calculated resolution.
Number images used: 22518

+
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