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Yorodumi- PDB-5xjb: The Crystal Structure of the Minimal Core Domain of the Microtubu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xjb | ||||||
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Title | The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with ADP-Mg-BeFx | ||||||
Components | Kinesin-like protein KIF2C | ||||||
Keywords | STRUCTURAL PROTEIN / Kinesin / Microtubule / tubulin / KIF2 / MCAK / depolymerization | ||||||
Function / homology | Function and homology information regulation of chromosome segregation / metaphase chromosome alignment / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / COPI-dependent Golgi-to-ER retrograde traffic ...regulation of chromosome segregation / metaphase chromosome alignment / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / COPI-dependent Golgi-to-ER retrograde traffic / Separation of Sister Chromatids / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / MHC class II antigen presentation / microtubule plus-end binding / microtubule depolymerization / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / chromosome, centromeric region / spindle / kinetochore / microtubule cytoskeleton / microtubule binding / microtubule / cell division / centrosome / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Ogawa, T. / Jiang, X. / Hirokawa, N. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Cell Rep / Year: 2017 Title: Mechanism of Catalytic Microtubule Depolymerization via KIF2-Tubulin Transitional Conformation Authors: Ogawa, T. / Saijo, S. / Shimizu, N. / Jiang, X. / Hirokawa, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xjb.cif.gz | 151.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xjb.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/5xjb ftp://data.pdbj.org/pub/pdb/validation_reports/xj/5xjb | HTTPS FTP |
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-Related structure data
Related structure data | 5xjaC 1v8kS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48453.543 Da / Num. of mol.: 2 / Fragment: UNP residues 184-585 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif2c / Production host: Escherichia coli (E. coli) / References: UniProt: Q922S8 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.9 Å3/Da / Density % sol: 57.62 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: potassium sodium tartrate tetrahydrate, MES, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 21151 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1561 / Rpim(I) all: 0.23 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V8K Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.892 / SU B: 19.877 / SU ML: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 172.98 Å2 / Biso mean: 79.629 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 3.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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