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Yorodumi- PDB-1kql: Crystal structure of the C-terminal region of striated muscle alp... -
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-Basic information
Entry | Database: PDB / ID: 1kql | ||||||
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Title | Crystal structure of the C-terminal region of striated muscle alpha-tropomyosin at 2.7 angstrom resolution | ||||||
Components | Fusion Protein of and striated muscle alpha-tropomyosin and the GCN4 leucine zipper | ||||||
Keywords | CONTRACTILE PROTEIN / thin filament / tropomyosin / muscle regulation / coiled coil / four-helix bundle | ||||||
Function / homology | Function and homology information Striated Muscle Contraction / Smooth Muscle Contraction / positive regulation of heart rate by epinephrine / bleb / negative regulation of vascular associated smooth muscle cell migration / muscle filament sliding / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding ...Striated Muscle Contraction / Smooth Muscle Contraction / positive regulation of heart rate by epinephrine / bleb / negative regulation of vascular associated smooth muscle cell migration / muscle filament sliding / 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 / actin filament capping / ruffle organization / nitrogen catabolite activation of transcription from RNA polymerase II promoter / positive regulation of ATP-dependent activity / sarcomere organization / ventricular cardiac muscle tissue morphogenesis / myofibril / negative regulation of vascular associated smooth muscle cell proliferation / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of cell adhesion / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / stress fiber / cardiac muscle contraction / positive regulation of stress fiber assembly / cellular response to amino acid starvation / cytoskeletal protein binding / negative regulation of cell migration / muscle contraction / actin filament organization / actin filament / wound healing / ruffle membrane / cellular response to reactive oxygen species / RNA polymerase II transcription regulator complex / : / disordered domain specific binding / actin filament binding / actin cytoskeleton / actin binding / regulation of cell shape / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / 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 / protein-containing complex / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Molecular replacement using a specially built model / Resolution: 2.7 Å | ||||||
Authors | Li, Y. / Mui, S. / Brown, J.H. / Strand, J. / Reshetnikova, L. / Tobacman, L.S. / Cohen, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: The crystal structure of the C-terminal fragment of striated-muscle alpha-tropomyosin reveals a key troponin T recognition site. Authors: Li, Y. / Mui, S. / Brown, J.H. / Strand, J. / Reshetnikova, L. / Tobacman, L.S. / Cohen, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kql.cif.gz | 33.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kql.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/1kql ftp://data.pdbj.org/pub/pdb/validation_reports/kq/1kql | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6603.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal methionine followed by sequence database residues 255-278 of GCN4 leucine zipper and then C-terminal sequence database residues 254-284 of rat striated muscle alpha-tropomyosin Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Rattus norvegicus (Norway rat) Genus: Saccharomyces, Rattus / Species: , / Strain: , / Plasmid: pET3d / Gene (production host): GCN4, ARG9 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 References: UniProt: P03069, GenBank: 207514, UniProt: P04692*PLUS #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: 4.12 Å3/Da / Density % sol: 70 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: PEG 550 monomethylether, glycerol, sodium chloride, magnesium acetate, bicine, tris buffer, dithiothreitol, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.909 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2001 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.909 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 7229 / Num. obs: 7221 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 82.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 9.14 / Num. unique all: 708 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 86920 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.217 |
-Processing
Software |
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Refinement | Method to determine structure: Molecular replacement using a specially built model Starting model: a specially built 56-residue two-stranded coiled-coil that contains a 24 residue fragment from the high resolution structure of the GCN4 leucine zipper Resolution: 2.7→44.91 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 93.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→44.91 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 9999 Å / Num. reflection obs: 6498 / % reflection Rfree: 8 % / Rfactor all: 0.2551 / Rfactor obs: 0.251 / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.251 | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.69 Å / Rfactor Rfree: 0.3353 / Rfactor Rwork: 0.3295 / Rfactor obs: 0.3295 |