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Yorodumi- PDB-6bbn: Crystal structure of a curved tubulin complex induced by the kine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bbn | |||||||||
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Title | Crystal structure of a curved tubulin complex induced by the kinesin-13 Kif2A | |||||||||
Components |
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Keywords | MOTOR PROTEIN / Kinesin / Kif2A / microtubules / tubulin / kinesin-13 | |||||||||
Function / homology | Function and homology information centriolar subdistal appendage / Kinesins / positive regulation of axon guidance / COPI-dependent Golgi-to-ER retrograde traffic / microtubule depolymerization / kinesin complex / microtubule motor activity / microtubule-based movement / mitotic spindle assembly / cytoskeletal motor activity ...centriolar subdistal appendage / Kinesins / positive regulation of axon guidance / COPI-dependent Golgi-to-ER retrograde traffic / microtubule depolymerization / kinesin complex / microtubule motor activity / microtubule-based movement / mitotic spindle assembly / cytoskeletal motor activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule / microtubule-based process / Mitotic Prometaphase / regulation of cell migration / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / centriole / cellular response to interleukin-4 / mitotic spindle organization / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / spindle pole / Separation of Sister Chromatids / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nervous system development / microtubule binding / microtubule / cell differentiation / nuclear body / protein heterodimerization activity / cell division / GTPase activity / centrosome / ubiquitin protein ligase binding / GTP binding / nucleolus / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.514 Å | |||||||||
Authors | Allingham, J.S. / Trofimova, D. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Ternary complex of Kif2A-bound tandem tubulin heterodimers represents a kinesin-13-mediated microtubule depolymerization reaction intermediate. Authors: Trofimova, D. / Paydar, M. / Zara, A. / Talje, L. / Kwok, B.H. / Allingham, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bbn.cif.gz | 460.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bbn.ent.gz | 364.9 KB | Display | PDB format |
PDBx/mmJSON format | 6bbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/6bbn ftp://data.pdbj.org/pub/pdb/validation_reports/bb/6bbn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 6 molecules ACBDPE
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947 #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 #3: Protein | | Mass: 17911.244 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) #4: Protein | | Mass: 47918.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2A, KIF2, KNS2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00139 |
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-Non-polymers , 5 types, 10 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-PO4 / | #9: Chemical | ChemComp-ANP / | |
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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: 3.2 Å3/Da / Density % sol: 61.57 % / Description: thin plates |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 8% PEG8000, 6% ethylene glycol, 10 mM DDT, 100 mM HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.46→50 Å / Num. obs: 40041 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 129.71 Å2 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.131 / Rrim(I) all: 0.249 / Χ2: 1.303 / Net I/σ(I): 4.5 / Num. measured all: 142449 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 4LNU & 2GRY Resolution: 3.514→49.217 Å / SU ML: 0.7 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 263.18 Å2 / Biso mean: 146.2432 Å2 / Biso min: 68.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.514→49.217 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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