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Yorodumi- PDB-1t0y: Solution Structure of a Ubiquitin-Like Domain from Tubulin-bindin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t0y | ||||||
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Title | Solution Structure of a Ubiquitin-Like Domain from Tubulin-binding Cofactor B | ||||||
Components | tubulin folding cofactor B | ||||||
Keywords | CHAPERONE / ubiquitin-like / cytoskeleton / microtubule / tubulin / CESG / Structural genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics | ||||||
Function / homology | Function and homology information post-chaperonin tubulin folding pathway / cell tip / tubulin complex assembly / microtubule plus-end / microtubule plus-end binding / microtubule associated complex / establishment of mitotic spindle orientation / alpha-tubulin binding / cytoplasmic microtubule organization / kinetochore ...post-chaperonin tubulin folding pathway / cell tip / tubulin complex assembly / microtubule plus-end / microtubule plus-end binding / microtubule associated complex / establishment of mitotic spindle orientation / alpha-tubulin binding / cytoplasmic microtubule organization / kinetochore / spindle pole / axon / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS, CARTESIAN MOLECULAR DYNAMICS IN EXPLICIT SOLVENT | ||||||
Authors | Lytle, B.L. / Peterson, F.C. / Qui, S.H. / Luo, M. / Volkman, B.F. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Solution Structure of a Ubiquitin-like Domain from Tubulin-binding Cofactor B. Authors: Lytle, B.L. / Peterson, F.C. / Qiu, S.H. / Luo, M. / Zhao, Q. / Markley, J.L. / Volkman, B.F. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t0y.cif.gz | 537.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t0y.ent.gz | 449 KB | Display | PDB format |
PDBx/mmJSON format | 1t0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t0y_validation.pdf.gz | 350 KB | Display | wwPDB validaton report |
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Full document | 1t0y_full_validation.pdf.gz | 484.6 KB | Display | |
Data in XML | 1t0y_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 1t0y_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/1t0y ftp://data.pdbj.org/pub/pdb/validation_reports/t0/1t0y | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13744.418 Da / Num. of mol.: 1 / Fragment: N-terminal ubiquitin-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: 5O73 or F53F4.3 / Plasmid: pQE30T / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009[pREP4] / References: UniProt: Q20728 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: CHEMICAL SHIFT ASSIGNMENTS WERE OBTAINED FROM STANDARD 3D TRIPLE-RESONANCE EXPERIMENTS, USING THE AUTOMATED METHOD OF GARANT (C. BARTELS) |
-Sample preparation
Details | Contents: 1 mM cofactor B ubiquitin-like domain U-15N, 13C; 20 mM sodium phosphate buffer; 50 mM NaCl Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 50 mM NaCl + 20 mM NaPO4 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS, CARTESIAN MOLECULAR DYNAMICS IN EXPLICIT SOLVENT Software ordinal: 1 Details: The C-terminal residues 91-120 were disordered (as evidenced by 15N relaxation data) and were excluded from the model. INITIAL STRUCTURES WERE GENERATED USING THE CANDID MODULE OF CYANA. ...Details: The C-terminal residues 91-120 were disordered (as evidenced by 15N relaxation data) and were excluded from the model. INITIAL STRUCTURES WERE GENERATED USING THE CANDID MODULE OF CYANA. ADDITIONAL NOE ASSIGNMENTS WERE DETERMINED MANUALLY. PHI AND PSI TORSION ANGLE CONSTRAINTS WERE GENERATED FROM CHEMICAL SHIFT DATABASE SEARCHING USING THE PROGRAM TALOS (G. CORNILESCU). | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |