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Yorodumi- PDB-1tjt: X-ray structure of the human alpha-actinin isoform 3 at 2.2A reso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tjt | ||||||
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Title | X-ray structure of the human alpha-actinin isoform 3 at 2.2A resolution | ||||||
Components | Alpha-actinin 3 | ||||||
Keywords | CONTRACTILE PROTEIN / Calponin homology domain / actin binding domain | ||||||
Function / homology | Function and homology information positive regulation of glucose catabolic process to lactate via pyruvate / negative regulation of relaxation of muscle / regulation of the force of skeletal muscle contraction / skeletal muscle atrophy / positive regulation of skeletal muscle fiber development / positive regulation of skeletal muscle tissue growth / response to denervation involved in regulation of muscle adaptation / positive regulation of fast-twitch skeletal muscle fiber contraction / transition between fast and slow fiber / positive regulation of bone mineralization involved in bone maturation ...positive regulation of glucose catabolic process to lactate via pyruvate / negative regulation of relaxation of muscle / regulation of the force of skeletal muscle contraction / skeletal muscle atrophy / positive regulation of skeletal muscle fiber development / positive regulation of skeletal muscle tissue growth / response to denervation involved in regulation of muscle adaptation / positive regulation of fast-twitch skeletal muscle fiber contraction / transition between fast and slow fiber / positive regulation of bone mineralization involved in bone maturation / muscle cell development / negative regulation of oxidative phosphorylation / focal adhesion assembly / Striated Muscle Contraction / bone morphogenesis / negative regulation of glycolytic process / Nephrin family interactions / negative regulation of cold-induced thermogenesis / negative regulation of calcineurin-NFAT signaling cascade / structural constituent of muscle / regulation of aerobic respiration / cortical actin cytoskeleton / pseudopodium / brush border / cell projection / actin filament / Z disc / actin filament binding / integrin binding / cell junction / actin cytoskeleton organization / regulation of apoptotic process / transmembrane transporter binding / focal adhesion / calcium ion binding / extracellular exosome / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Franzot, G. / Sjoblom, B. / Gautel, M. / Djinovic Carugo, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: The crystal structure of the actin binding domain from alpha-actinin in its closed conformation: structural insight into phospholipid regulation of alpha-actinin Authors: Franzot, G. / Sjoblom, B. / Gautel, M. / Djinovic Carugo, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tjt.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tjt.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 1tjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tjt_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
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Full document | 1tjt_full_validation.pdf.gz | 433 KB | Display | |
Data in XML | 1tjt_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1tjt_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/1tjt ftp://data.pdbj.org/pub/pdb/validation_reports/tj/1tjt | HTTPS FTP |
-Related structure data
Related structure data | 1wkuC 1bkrS 1qagS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 28620.836 Da / Num. of mol.: 1 / Fragment: actin binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08043 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: peg 4000, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→34.61 Å / Num. all: 11674 / Num. obs: 11674 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 8.6 Å2 / Rmerge(I) obs: 0.089 |
Reflection shell | Resolution: 2.19→2.33 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.186 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QAG for CH1 domain and 1BKR for CH2 domain Resolution: 2.19→34.61 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 867794.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.0791 Å2 / ksol: 0.35091 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.19→34.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.33 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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