[English] 日本語
Yorodumi- PDB-2efs: Crystal structure of the C-terminal tropomyosin fragment with N- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2efs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the C-terminal tropomyosin fragment with N- and C-terminal extensions of the leucine zipper at 2.0 angstroms resolution | ||||||
Components | General control protein GCN4 and Tropomyosin 1 alpha chain | ||||||
Keywords | CONTRACTILE PROTEIN / DESTABILIZING CLUSTER / HYDROPHOBIC CORE | ||||||
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 / troponin I binding / TFIID-class transcription factor complex binding / amino acid biosynthetic process ...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 / troponin I binding / 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 / actin filament / RNA polymerase II transcription regulator complex / : / actin filament binding / actin cytoskeleton / 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 / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2 Å | ||||||
Authors | Minakata, S. / Nitanai, Y. / Maeda, K. / Oda, N. / Wakabayashi, K. / Maeda, Y. | ||||||
Citation | Journal: To be Published Title: Two crystal structures of tropomyosin C-terminal fragment 176-273: exposure of the hydrophobic core to the solvent destabilizes the tropomyosin molecule Authors: Minakata, S. / Nitanai, Y. / Maeda, K. / Oda, N. / Wakabayashi, K. / Maeda, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2efs.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2efs.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 2efs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2efs ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2efs | HTTPS FTP |
---|
-Related structure data
Related structure data | 2efrC 2d3eS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18338.695 Da / Num. of mol.: 4 / Fragment: residues 147-175, residues 176-301 / Mutation: C190S Source method: isolated from a genetically manipulated source Details: N-TERMINAL METHIONINE FOLLOWED BY SEQUENCE DATABASE RESIDUES 249-277 OF GCN4 LEUCINE ZIPPER AND THEN C-TERMINAL SEQUENCE DATABASE RESIDUES 176-273 OF RABBIT SKELETAL MUSCLE ALPHA-TROPOMYOSIN Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Oryctolagus cuniculus (rabbit) Genus: Saccharomyces, Oryctolagus / Species: , / Strain: , / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03069, UniProt: P58772 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 40% MPD, 0.4M AMMONIUM ACETATE 0.1M TRIS-HCL, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 13, 2005 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.25 Å / Num. all: 47224 / Num. obs: 47224 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.87 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.66 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 4.8 / % possible all: 93.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: molecular replacement Starting model: 2D3E Resolution: 2→19.92 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 961824.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.0367 Å2 / ksol: 0.337962 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.9 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.92 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|