+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ig9 | ||||||
---|---|---|---|---|---|---|---|
Title | Tra1 subunit from Saccharomyces cerevisiae SAGA complex | ||||||
![]() | Transcription-associated protein 1 | ||||||
![]() | TRANSCRIPTION / Epigenetics / Acetyltransferase / Co-activator | ||||||
Function / homology | ![]() SLIK (SAGA-like) complex / SAGA complex / NuA4 histone acetyltransferase complex / Ub-specific processing proteases / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
![]() | Zheng, X.D. / Liu, G.C. / Guan, H.P. / Li, H.T. | ||||||
![]() | ![]() 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 / ![]() | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 492.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 333.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 930.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 949.9 KB | Display | |
Data in XML | ![]() | 81.7 KB | Display | |
Data in CIF | ![]() | 134.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9664MC ![]() 9663C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 433677.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Tra1 / ScTra1 / Type: COMPLEX Details: One of the major part from SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex Entity ID: all / Source: NATURAL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 1.8 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||
Buffer solution | pH: 8.5 / Details: 20mM HEPES pH 8.5 150mM Nacl | ||||||||||||
Buffer component |
| ||||||||||||
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: We extracted it from the overall SAGA complex structure. | ||||||||||||
Specimen support | Details: The grid was coated with a home-made thin continuous carbon film. Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K Details: Blot for 4 seconds and wait for 30 seconds before plunging |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm / Cs: 0.1 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K |
Image recording | Average exposure time: 0.25 sec. / Electron dose: 5.6 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8526 |
EM imaging optics | Spherical aberration corrector: With a Cs-corrector |
Image scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 3-30 |
-
Processing
Software | Name: PHENIX / Version: dev_3290: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: GPU accelerated / Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1350000 / Details: GPU accelerated | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176464 / Algorithm: FOURIER SPACE / Details: GPU accelerated / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OJS Accession code: 5OJS / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|