[English] 日本語
- EMDB-9663: Saccharomyces cerevisiae SAGA complex -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: EMD-9663
TitleSaccharomyces cerevisiae SAGA complex
Map data
SampleSaccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsZheng XD / Liu GC / Guan HP / Li HT
CitationJournal: Cell Discov / Year: 2019
Title: Architecture of SAGA complex.
Authors: Gaochao Liu / Xiangdong Zheng / Haipeng Guan / Yong Cao / Hongyuan Qu / Junqing Kang / Xiangle Ren / Jianlin Lei / Meng-Qiu Dong / Xueming Li / Haitao Li /
DateDeposition: Sep 25, 2018 / Header (metadata) release: May 15, 2019 / Map release: May 15, 2019 / Update: May 22, 2019

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_9663.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 360 pix.
= 504.36 Å
1.4 Å/pix.
x 360 pix.
= 504.36 Å
1.4 Å/pix.
x 360 pix.
= 504.36 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.401 Å
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.04819569 - 0.11833755
Average (Standard dev.)0.0003225751 (±0.0028834597)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 504.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4011.4011.401
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z504.360504.360504.360
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0480.1180.000

Supplemental data

Mask #1

Projections & Slices


Slices (1/2)
Density Histograms

Sample components

Entire Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex

EntireName: Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex
Details: The multi-functional co-activator SAGA complex / Number of components: 1

Component #1: protein, Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransf...

ProteinName: Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex
Details: The multi-functional co-activator SAGA complex / Recombinant expression: No
MassTheoretical: 1.8 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BYL4741
Source (natural)Organelle: Nucleus / Location in cell: Nucleus

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / Buffer solution: 20mM HEPES pH 8.5 150mM Nacl / pH: 8.5
Support filmThe grid was coated with a home-made thin continuous carbon film.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 95 %

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5.6 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000.0 X (nominal), 81000.0 X (calibrated) / Cs: 0.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (70.0 - 70.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 8526 / Sampling size: 5 µm

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 176464 / Details: Cs-corrector was used for data collection
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / CTF correction: GPU accelerated Gctf / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF
Euler angles: Several rounds of refinement were used to get the best results.
FSC plot (resolution estimation)

About Yorodumi


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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more


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.

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