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Yorodumi- PDB-5lb7: Complex structure between p60N/p80C katanin and a peptide derived... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lb7 | ||||||
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Title | Complex structure between p60N/p80C katanin and a peptide derived from ASPM | ||||||
Components |
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Keywords | HYDROLASE / katanin / ASPM / severing enzyme | ||||||
Function / homology | Function and homology information negative regulation of asymmetric cell division / forebrain neuroblast division / ATPase regulator activity / katanin complex / spindle localization / microtubule minus-end / meiotic spindle assembly / maintenance of centrosome location / microtubule-severing ATPase / microtubule severing ATPase activity ...negative regulation of asymmetric cell division / forebrain neuroblast division / ATPase regulator activity / katanin complex / spindle localization / microtubule minus-end / meiotic spindle assembly / maintenance of centrosome location / microtubule-severing ATPase / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole / microtubule severing / positive regulation of microtubule depolymerization / regulation of meiotic cell cycle / neuronal stem cell population maintenance / negative regulation of microtubule depolymerization / microtubule bundle formation / meiotic spindle / microtubule depolymerization / spindle organization / Cul3-RING ubiquitin ligase complex / dynein complex binding / oogenesis / positive regulation of neuroblast proliferation / mitotic spindle pole / negative regulation of neuron differentiation / developmental growth / cytoplasmic microtubule organization / isomerase activity / lipid droplet / neuron migration / protein localization / brain development / cerebral cortex development / positive regulation of neuron projection development / spindle pole / spindle / male gonad development / microtubule cytoskeleton / positive regulation of canonical Wnt signaling pathway / negative regulation of neuron projection development / midbody / growth cone / spermatogenesis / microtubule binding / microtubule / calmodulin binding / positive regulation of apoptotic process / cell cycle / apical plasma membrane / protein heterodimerization activity / cell division / axon / centrosome / neuronal cell body / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Rezabkova, L. / Capitani, G. / Kammerer, R.A. / Steinmetz, M.O. | ||||||
Citation | Journal: Nat. Cell Biol. / Year: 2017 Title: Microtubule minus-end regulation at spindle poles by an ASPM-katanin complex. Authors: Jiang, K. / Rezabkova, L. / Hua, S. / Liu, Q. / Capitani, G. / Maarten Altelaar, A.F. / Heck, A.J.R. / Kammerer, R.A. / Steinmetz, M.O. / Akhmanova, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lb7.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lb7.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 5lb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lb7_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 5lb7_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 5lb7_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 5lb7_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/5lb7 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/5lb7 | HTTPS FTP |
-Related 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: 23351.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Katnb1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BG40 |
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#2: Protein | Mass: 9534.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Katna1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WV86, EC: 3.6.4.3 |
#3: Protein/peptide | Mass: 1007.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8CJ27 |
#4: 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: 2.09 Å3/Da / Density % sol: 41.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 20% PEG 3350, 0.1 M BisTris propane, 0.2 M NaNO3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 45112 / % possible obs: 97.7 % / Redundancy: 24.6 % / Net I/σ(I): 19.8 |
-Processing
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Refinement | Resolution: 1.5→43.868 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→43.868 Å
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Refine LS restraints |
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LS refinement shell |
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