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Yorodumi- PDB-1dgc: THE X-RAY STRUCTURE OF THE GCN4-BZIP BOUND TO ATF/CREB SITE DNA S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dgc | ||||||
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Title | THE X-RAY STRUCTURE OF THE GCN4-BZIP BOUND TO ATF/CREB SITE DNA SHOWS THE COMPLEX DEPENDS ON DNA FLEXIBILITY | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX | ||||||
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 / Resolution: 3 Å | ||||||
Authors | Koenig, P. / Richmond, T.J. | ||||||
Citation | 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: Konig, P. / Richmond, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dgc.cif.gz | 35.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dgc.ent.gz | 21.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dgc_validation.pdf.gz | 369.7 KB | Display | wwPDB validaton report |
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Full document | 1dgc_full_validation.pdf.gz | 379 KB | Display | |
Data in XML | 1dgc_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1dgc_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/1dgc ftp://data.pdbj.org/pub/pdb/validation_reports/dg/1dgc | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 0 -1 0 X 117.32 X SYMM -1 0 0 Y + 117.32 = Y SYMM 0 0 -1 Z 43.33 Z SYMM |
-Components
#1: DNA chain | Mass: 5820.771 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 7244.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069 |
Sequence details | AMINO ACIDS NUMBERING (RESIDUE NUMBER) CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density meas: 1.28 Mg/m3 / Density % sol: 56.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | Resolution: 3→20 Å |
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Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / % possible obs: 99 % / Rmerge(I) obs: 0.09 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3→10 Å / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 3296 / σ(F): 3 / Rfactor obs: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.86 |