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- PDB-1ysa: THE GCN4 BASIC REGION LEUCINE ZIPPER BINDS DNA AS A DIMER OF UNIN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ysa | ||||||
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Title | THE GCN4 BASIC REGION LEUCINE ZIPPER BINDS DNA AS A DIMER OF UNINTERRUPTED ALPHA HELICES: CRYSTAL STRUCTURE OF THE PROTEIN-DNA COMPLEX | ||||||
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![]() | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() 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 transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Ellenberger, T.E. / Brandl, C.J. / Struhl, K. / Harrison, S.C. | ||||||
![]() | ![]() 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. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.6 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 380.6 KB | Display | ![]() |
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Full document | ![]() | 416.9 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: TWO ADENINES, B 22 AND B 23, ARE NEAR THE 5-PRIME END OF DNA CHAIN B AND ARE LOOPED OUT OF THE DNA HELIX. THIS CONFORMATION IS PRESENT IN CRYSTALS THAT WERE SOAKED IN 35% (VOL/VOL) POLYETHYLENE ...1: TWO ADENINES, B 22 AND B 23, ARE NEAR THE 5-PRIME END OF DNA CHAIN B AND ARE LOOPED OUT OF THE DNA HELIX. THIS CONFORMATION IS PRESENT IN CRYSTALS THAT WERE SOAKED IN 35% (VOL/VOL) POLYETHYLENE GLYCOL MW 400, FOLLOWED BY RAPID FREEZING AND X-RAY DATA COLLECTION AT -155 DEGREES CENTIGRADE. |
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Components
#1: DNA chain | Mass: 6034.915 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 6231.067 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 6892.072 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K TWO ADENINES, B22 AND B23, WHICH ARE NEAR THE 5-PRIME END OF DNA CHAIN B ARE LOOPED OUT OF THE DNA HELIX. THIS CONFORMATION IS ...Details: pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K TWO ADENINES, B22 AND B23, WHICH ARE NEAR THE 5-PRIME END OF DNA CHAIN B ARE LOOPED OUT OF THE DNA HELIX. THIS CONFORMATION IS PRESENT IN CRYSTALS THAT WERE SOAKED IN 35% (VOL/VOL) POLYETHYLENE GLYCOL MW 400, FOLLOWED BY RAPID FREEZING AND X-RAY DATA COLLECTION AT -155 DEG. CENTIGRADE. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusionDetails: well solution contains twice the concentrations of salts and PEG400 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 118 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS-NICOLET / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→8 Å / Num. obs: 5289 / % possible obs: 96 % / Observed criterion σ(F): 1.5 / Rmerge(I) obs: 0.099 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Observed criterion σ(F): 1.5 / Num. measured all: 21237 / Rmerge(I) obs: 0.099 |
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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.9→8 Å / σ(F): 1.5 /
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Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 5289 / Rfactor obs: 0.23 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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