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Yorodumi- PDB-2d3e: Crystal structure of the C-Terminal fragment of rabbit skeletal a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d3e | ||||||
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Title | Crystal structure of the C-Terminal fragment of rabbit skeletal alpha-tropomyosin | ||||||
Components | General control protein GCN4 and Tropomyosin 1 alpha chain | ||||||
Keywords | CONTRACTILE PROTEIN / COILED COIL / ALANINE CLUSTER / BENDABLE REGION | ||||||
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: 2.6 Å | ||||||
Authors | Nitanai, Y. / Maeda, K. / Oda, N. / Minakata, S. / Maeda, Y. | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of C-Terminal Fragment of Rabbit Skeletal Alpha-Tropomyosin; Crystallographic Evidence of Tropomyosin Bending Authors: Nitanai, Y. / Maeda, K. / Oda, N. / Minakata, S. / Maeda, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d3e.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d3e.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/2d3e ftp://data.pdbj.org/pub/pdb/validation_reports/d3/2d3e | HTTPS FTP |
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-Related structure data
Related structure data | 1ic2S S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 15651.484 Da / Num. of mol.: 4 / Fragment: residues 151-175, residues 176-284 Source method: isolated from a genetically manipulated source Details: N-TERMINAL METHIONINE FOLLOWED BY SEQUENCE DATABASE RESIDUES 254-278 OF GCN4 LEUCINE ZIPPER AND THEN C-TERMINAL SEQUENCE DATABASE RESIDUES 176-284 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: MPD, AMMONIUM ACETATE, SODIUM CITRATE, pH 5.20, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 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: 2.6→45.67 Å / Num. all: 19366 / Num. obs: 19366 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.56 % / Biso Wilson estimate: 83.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 17 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 9 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB CODE 1IC2 Resolution: 2.6→45.67 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 701605.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: NCS GROUP 1 INCLUDES MAIN CHAIN ATOMS OF CHAIN A AND C, NCS GROUP 2 INCLUDES MAIN CHAIN ATOMS OF CHAIN B AND D
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.558 Å2 / ksol: 0.312812 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→45.67 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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