[English] 日本語
Yorodumi- PDB-1ij1: GCN4-pVLT Coiled-coil Trimer with Threonine at the d(12) Position -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ij1 | ||||||
---|---|---|---|---|---|---|---|
Title | GCN4-pVLT Coiled-coil Trimer with Threonine at the d(12) Position | ||||||
Components | GENERAL CONTROL PROTEIN GCN4 | ||||||
Keywords | TRANSCRIPTION / GCN4 / coiled coil | ||||||
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 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Akey, D.L. / Malashkevich, V.N. / Kim, P.S. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Buried polar residues in coiled-coil interfaces. Authors: Akey, D.L. / Malashkevich, V.N. / Kim, P.S. #1: 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. #2: 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. #3: Journal: Nat.Struct.Biol. / Year: 1996 Title: Buried polar residues and structural specificity in the GCN4 leucine zipper Authors: Gonzalez Jr., L. / Woolfson, D.N. / Alber, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ij1.cif.gz | 31.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ij1.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ij1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/1ij1 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/1ij1 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 4004.676 Da / Num. of mol.: 3 / Fragment: COILED COIL REGION / Mutation: L12T, N16V / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. IT IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE (YEAST). THE PEPTIDE is a variant of the yeast GCN4 coiled coil region made by solid phase synthesis. References: UniProt: P03069 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.34 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Na Cacodylate, 20% PEG 8000, 0.2 M Zn Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS Method: sparse matrix method | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 8488 / Num. obs: 8284 / % possible obs: 97.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.86→1.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 4.5 / % possible all: 87.8 |
Reflection | *PLUS Highest resolution: 1.86 Å / Num. measured all: 80296 |
Reflection shell | *PLUS % possible obs: 94.4 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 472116.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.48 Å2 / ksol: 0.292 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.86→1.93 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 9
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.378 / % reflection Rfree: 8.9 % / Rfactor Rwork: 0.31 |