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- EMDB-9664: Tra1 subunit from Saccharomyces cerevisiae SAGA complex -

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Basic information

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

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

Downloads & links


FileDownload / File: emd_9664.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: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.052679177 - 0.122503795
Average (Standard dev.)0.00017765604 (±0.0025359453)
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-0.0530.1230.000

Supplemental data

Mask #1

Projections & Slices


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

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