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Yorodumi- PDB-2dgc: GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dgc | ||||||
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Title | GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / BASIC DOMAIN / LEUCINE ZIPPER / DNA BINDING / EUKARYOTIC REGULATORY PROTEIN / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information protein localization to nuclear periphery / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA 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 / Resolution: 2.2 Å | ||||||
Authors | Keller, W. / Koenig, P. / Richmond, T.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition. Authors: Keller, W. / Konig, P. / Richmond, T.J. #1: Journal: J.Mol.Biol. / Year: 1993 Title: The X-Ray Structure of the GCN4-bZIP Bound to ATF/CREB Site DNA Shows the Complex Depends on DNA Flexibility Authors: Koenig, P. / Richmond, T.J. #2: Journal: Cell(Cambridge,Mass.) / Year: 1992 Title: The GCN4 Basic Region Leucine Zipper Binds DNA as a Dimer of Uninterrupted Alpha Helices: Crystal Structure of the Protein-DNA Complex Authors: Ellenberger, T.E. / Brandl, C.J. / Struhl, K. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dgc.cif.gz | 37.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dgc.ent.gz | 23 KB | Display | PDB format |
PDBx/mmJSON format | 2dgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/2dgc ftp://data.pdbj.org/pub/pdb/validation_reports/dg/2dgc | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE ASYMMETRIC UNIT CONTAINS ONE HALF OF PROTEIN/DNA COMPLEX PER ASYMMETRIC UNIT. MOLECULAR DYAD AXIS OF PROTEIN DIMER AND PALINDROMIC HALF SITES OF THE DNA COINCIDES WITH CRYSTALLOGRAPHIC TWO-FOLD AXIS. THE FULL PROTEIN/DNA COMPLEX CAN BE OBTAINED BY APPLYING THE FOLLOWING TRANSFORMATION MATRIX AND TRANSLATION VECTOR TO THE COORDINATES X Y Z: SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: A 229 .. 277 APPLIED TO RESIDUES: B -10 .. 9 SYMMETRY1 1 0.000000 -1.000000 0.000000 117.32000 SYMMETRY2 1 -1.000000 0.000000 0.000000 117.32000 SYMMETRY3 1 0.000000 0.000000 -1.000000 43.44000 |
-Components
#1: DNA chain | Mass: 5820.771 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 7375.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069 |
#3: Water | ChemComp-HOH / |
Sequence details | AMINO ACID NUMBERING (RESIDUE NUMBER) CORRESPONDS TO THE 281 AMINO ACIDS OF INTACT GCN4. RESIDUE ...AMINO ACID NUMBERING (RESIDUE NUMBER) CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.82 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 4.6 / Details: pH 4.60, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: unknown / pH: 4.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 6597 / % possible obs: 80.8 % / Observed criterion σ(F): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.09 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 15 Å / % possible obs: 80.8 % / Observed criterion σ(F): 3 |
-Processing
Software |
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Refinement | Resolution: 2.2→6 Å / σ(F): 3
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Displacement parameters | Biso mean: 41.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARAM11.DNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 6 Å / σ(F): 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.3 Å2 |