[English] 日本語
Yorodumi- PDB-4rgw: Crystal Structure of a TAF1-TAF7 Complex in Human Transcription F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rgw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a TAF1-TAF7 Complex in Human Transcription Factor IID | ||||||
Components |
| ||||||
Keywords | Transferase/Transcription / triple barrel / winged helix / transcriptional regulation / DNA binding / Phosphorylation / nucleus / Transferase-Transcription complex | ||||||
Function / homology | Function and homology information spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of androgen receptor activity / nuclear vitamin D receptor binding ...spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of androgen receptor activity / nuclear vitamin D receptor binding / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / nuclear thyroid hormone receptor binding / cellular response to ATP / histone acetyltransferase binding / midbrain development / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / ubiquitin conjugating enzyme activity / MLL1 complex / transcription initiation at RNA polymerase I promoter / P-TEFb complex binding / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / intracellular estrogen receptor signaling pathway / regulation of DNA repair / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / negative regulation of ubiquitin-dependent protein catabolic process / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / male germ cell nucleus / regulation of signal transduction by p53 class mediator / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / protein polyubiquitination / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of protein binding / kinase activity / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / protein autophosphorylation / protein stabilization / transcription cis-regulatory region binding / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / protein heterodimerization activity / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å | ||||||
Authors | Wang, H. / Curran, E.C. / Hinds, T.R. / Wang, E.H. / Zheng, N. | ||||||
Citation | Journal: Cell Res. / Year: 2014 Title: Crystal structure of a TAF1-TAF7 complex in human transcription factor IID reveals a promoter binding module. Authors: Wang, H. / Curran, E.C. / Hinds, T.R. / Wang, E.H. / Zheng, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4rgw.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4rgw.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 4rgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/4rgw ftp://data.pdbj.org/pub/pdb/validation_reports/rg/4rgw | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 73418.359 Da / Num. of mol.: 1 / Fragment: DUF3591 domain, UNP residues 579-1215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High Five References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase | ||
---|---|---|---|
#2: Protein | Mass: 40412.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF7, TAF2F, TAFII55 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High Five / References: UniProt: Q15545 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2 M potassium sodium tartrate tetrahydrate, pH 7.4, 20% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2012 |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 36320 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1776 / % possible all: 96.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.301→47.271 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 21.97 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.301→47.271 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|