[English] 日本語
Yorodumi
- EMDB-9664: Tra1 subunit from Saccharomyces cerevisiae SAGA complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: EMD-9664
TitleTra1 subunit from Saccharomyces cerevisiae SAGA complex
Map data
SampleTra1 / ScTra1:
Transcription-associated protein 1
Function / homology
Function and homology information


Ub-specific processing proteases / ASTRA complex / SLIK (SAGA-like) complex / SAGA complex / NuA4 histone acetyltransferase complex / transcription coregulator activity / histone acetylation / DNA repair / regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / nucleus
PIK-related kinase, FAT / PIK-related kinase / FATC domain profile. / FAT domain profile. / FAT domain / Phosphatidylinositol 3- and 4-kinase / Transcription-associated protein 1 / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-type fold / FATC domain / Protein kinase-like domain superfamily
Transcription-associated protein 1
SourceSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 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 /
Validation ReportPDB-ID: 6ig9

SummaryFull reportAbout validation report
DateDeposition: Sep 25, 2018 / Header (metadata) release: May 15, 2019 / Map release: May 15, 2019 / Update: May 22, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6ig9
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_9664.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.401 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.052679177 - 0.122503795
Average (Standard dev.)0.00017765604 (±0.0025359453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
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
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0530.1230.000

-
Supplemental data

-
Mask #1

Fileemd_9664_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire Tra1 / ScTra1

EntireName: Tra1 / ScTra1
Details: One of the major part from SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex
Number of components: 2

-
Component #1: protein, Tra1 / ScTra1

ProteinName: Tra1 / ScTra1
Details: One of the major part from SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex
Recombinant expression: No
MassTheoretical: 1.8 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (natural)Organelle: Nucleus / Location in cell: nucleus

-
Component #2: protein, Transcription-associated protein 1

ProteinName: Transcription-associated protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 433.677281 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: BYL4741

-
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 %
Details: Blot for 4 seconds and wait for 30 seconds before plunging.

-
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
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / CTF correction: GPU accelerated / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Details: GPU accelerated / Euler angles: GPU accelerated
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 5OJS
Output model

+
About Yorodumi

-
News

-
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

-
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.

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