+Open data
-Basic information
Entry | Database: PDB / ID: 2z5i | ||||||
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Title | Crystal structure of the head-to-tail junction of tropomyosin | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / actin / troponin / tropomyosin / cytoskeleton / cardiomyopathy | ||||||
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: 2.1 Å | ||||||
Authors | Murakami, K. / Nozawa, K. / Tomii, K. / Kudou, N. / Igarashi, N. / Shirakihara, Y. / Wakatsuki, S. / Stewart, M. / Yasunaga, T. / Wakabayashi, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Structural basis for tropomyosin overlap in thin (actin) filaments and the generation of a molecular swivel by troponin-T Authors: Murakami, K. / Stewart, M. / Nozawa, K. / Tomii, K. / Kudou, N. / Igarashi, N. / Shirakihara, Y. / Wakatsuki, S. / Yasunaga, T. / Wakabayashi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z5i.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z5i.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 2z5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/2z5i ftp://data.pdbj.org/pub/pdb/validation_reports/z5/2z5i | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 2
NCS ensembles :
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-Components
#1: Protein | Mass: 6056.825 Da / Num. of mol.: 8 Fragment: C terminal domain of GCN4 and Tropomyosin alpha-1 chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Oryctolagus cuniculus (rabbit) Genus: Saccharomyces, Oryctolagus / Species: , / Strain: , / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P03069, UniProt: P58772 #2: Protein/peptide | Mass: 4537.393 Da / Num. of mol.: 2 Fragment: N terminal domain of Tropomyosin alpha-1 chain and C terminal domain of GCN4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Genus: Oryctolagus, Saccharomyces / Species: , / Strain: , / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P58772, UniProt: P03069 #3: Chemical | #4: 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: 2.72 Å3/Da / Density % sol: 54.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→65 Å / Num. obs: 35852 / % possible obs: 96.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.78 / Num. unique all: 3426 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.92 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.962 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.222 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→32.92 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.099→2.154 Å / Total num. of bins used: 20
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