[English] 日本語
Yorodumi- PDB-1uo4: Structure Based Engineering of Internal Molecular Surfaces Of Fou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uo4 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles | ||||||
Components | GENERAL CONTROL PROTEIN GCN4 | ||||||
Keywords | FOUR HELIX BUNDLE / CAVITY / IODOBENZENE | ||||||
Function / homology | Function and homology information protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / cellular response to nutrient levels / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Yadav, M.K. / Redman, J.E. / Alvarez-Gutierrez, J.M. / Zhang, Y. / Stout, C.D. / Ghadiri, M.R. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structure-Based Engineering of Internal Cavities in Coiled-Coil Peptides Authors: Yadav, M.K. / Redman, J.E. / Leman, L.J. / Alvarez-Gutierrez, J.M. / Zhang, Y. / Stout, C.D. / Ghadiri, M.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1uo4.cif.gz | 24.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1uo4.ent.gz | 17 KB | Display | PDB format |
PDBx/mmJSON format | 1uo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uo4_validation.pdf.gz | 388.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1uo4_full_validation.pdf.gz | 388.8 KB | Display | |
Data in XML | 1uo4_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 1uo4_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/1uo4 ftp://data.pdbj.org/pub/pdb/validation_reports/uo/1uo4 | HTTPS FTP |
-Related structure data
Related structure data | 1untC 1unuC 1unvC 1unwC 1unxC 1unyC 1unzC 1uo0C 1uo1C 1uo2C 1uo3C 1uo5C 1w5gC 1w5iC 2bniC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 4016.732 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically Details: BASED ON SEQUENCE FROM SACCHAROMYCES CEREVISIAE (BAKER'S YEAST) Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069 #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-PIH / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROP, RESERVOIR: 10%W/V PEG 6K, 2 M NACL, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 114 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.82 |
Detector | Date: Feb 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→55.902 Å / Num. obs: 9782 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 19.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.5 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→55.9 Å / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.109
| ||||||||||||||||||||
Displacement parameters | Biso mean: 37.213 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→55.9 Å
|