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Yorodumi- PDB-1rb6: ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rb6 | ||||||
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Title | ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TETRAGONAL FORM | ||||||
Components | General control protein GCN4 | ||||||
Keywords | DNA BINDING PROTEIN / COILED COIL / LEUCINE ZIPPER | ||||||
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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Holton, J. / Alber, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Automated protein crystal structure determination using ELVES. Authors: Holton, J. / Alber, T. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: An Engineered Allosteric Switch in Leucine-Zipper Oligomerization Authors: Gonzalez Jr., L. / Plecs, J.J. / Alber, T. #2: Journal: Nature / Year: 1994 Title: Crystal Structure of an Isoleucine-Zipper Trimer Authors: Harbury, P.B. / Kim, P.S. / Alber, T. #3: Journal: Science / Year: 1993 Title: A Switch between Two-, Three-, and Four-Stranded Coiled Coils in GCN4 Leucine Zipper Mutants Authors: Harbury, P.B. / Zhang, T. / Kim, P.S. / Alber, T. #4: Journal: Science / Year: 1991 Title: X-Ray Structure of the GCN4 Leucine Zipper, a two-stranded, parallel coiled coil. Authors: O'Shea, E.K. / Klemm, J.D. / Kim, P.S. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rb6.cif.gz | 34.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rb6.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rb6_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
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Full document | 1rb6_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 1rb6_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 1rb6_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/1rb6 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/1rb6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3988.677 Da / Num. of mol.: 3 / Fragment: LEUCINE-ZIPPER (RESIDUES 249-281) / Mutation: N16A / Source method: obtained synthetically Details: The sequence of the protein is naturally found in Saccharomyces cerevisiae. The protein was chemically synthesized. References: UniProt: P03069 #2: Chemical | ChemComp-CL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 75 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 25 mM phosphate 400 mM NaCl 15% PEG8000, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.0688, 0.9800, 0.9797, 0.9795, 0.9322 | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 1998 | ||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→45 Å / Num. all: 20031 / Num. obs: 19898 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Version: 4 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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