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Yorodumi- PDB-5jx1: The neck-linker and alpha 7 helix of Mus musculus KIF3A fused to EB1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jx1 | ||||||
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Title | The neck-linker and alpha 7 helix of Mus musculus KIF3A fused to EB1 | ||||||
Components | Chimera protein of Kinesin-like protein KIF3A and Microtubule-associated protein RP/EB family member 1 | ||||||
Keywords | MOTOR PROTEIN / kinesin / coiled-coil | ||||||
Function / homology | Function and homology information epidermal stem cell homeostasis / positive regulation of axo-dendritic protein transport / positive regulation of establishment or maintenance of cell polarity regulating cell shape / kinesin II complex / intraciliary transport particle B binding / alpha-tubulin acetylation / Activation of SMO / Intraflagellar transport / protein localization to astral microtubule / cortical microtubule cytoskeleton ...epidermal stem cell homeostasis / positive regulation of axo-dendritic protein transport / positive regulation of establishment or maintenance of cell polarity regulating cell shape / kinesin II complex / intraciliary transport particle B binding / alpha-tubulin acetylation / Activation of SMO / Intraflagellar transport / protein localization to astral microtubule / cortical microtubule cytoskeleton / centriole-centriole cohesion / mitotic spindle astral microtubule end / microtubule anchoring at centrosome / positive regulation of keratinocyte proliferation / cilium movement / motile cilium assembly / protein localization to cell junction / Kinesins / ribbon synapse / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / COPI-dependent Golgi-to-ER retrograde traffic / protein localization to microtubule / Hedgehog 'off' state / microtubule plus-end / dorsal/ventral neural tube patterning / cell projection membrane / positive regulation of intracellular protein transport / attachment of mitotic spindle microtubules to kinetochore / dentate gyrus development / MHC class II antigen presentation / microtubule plus-end binding / anterograde axonal transport / non-motile cilium assembly / neural precursor cell proliferation / microtubule bundle formation / dorsal/ventral pattern formation / motile cilium / determination of left/right symmetry / protein localization to centrosome / neural tube development / microtubule organizing center / anterior/posterior pattern specification / negative regulation of microtubule polymerization / kinesin complex / microtubule motor activity / smoothened signaling pathway / spectrin binding / heart looping / mitotic spindle pole / microtubule polymerization / axoneme / establishment of mitotic spindle orientation / kinesin binding / cilium assembly / keratinocyte proliferation / spindle assembly / regulation of microtubule polymerization or depolymerization / epidermis development / spindle midzone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / forebrain development / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / ciliary basal body / kidney development / positive regulation of epithelial cell proliferation / RHO GTPases Activate Formins / spindle microtubule / protein localization / cilium / small GTPase binding / positive regulation of receptor-mediated endocytosis / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / cell migration / protein transport / heart development / microtubule binding / protein phosphatase binding / in utero embryonic development / microtubule / molecular adaptor activity / neuron projection / cadherin binding / cell division / focal adhesion Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Phillips, R.K. / Rayment, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Family-specific Kinesin Structures Reveal Neck-linker Length Based on Initiation of the Coiled-coil. Authors: Phillips, R.K. / Peter, L.G. / Gilbert, S.P. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jx1.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jx1.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 5jx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/5jx1 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/5jx1 | HTTPS FTP |
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-Related structure data
Related structure data | 5jv3C 5jvmC 5jvpC 5jvrC 5jvsC 5jvuC 1yibS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 8923.008 Da / Num. of mol.: 1 Fragment: UNP P28741 residues 352-376,UNP Q15691 residues 210-257 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Gene: Kif3a, Kif3, MAPRE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28741, UniProt: Q15691 |
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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: 1.9 Å3/Da / Density % sol: 35.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 24% (w/v) 2-methyl-2,4-pentanediol (MPD), 10% (w/v) PEG 4000, 100 mM CaCl2, 100 mM (3-(N-morpholino)propanesulfonic acid) (MOPS) pH 7.0, 1 mM CdCl2 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→39.82 Å / Num. obs: 14745 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 50.1 |
Reflection shell | Resolution: 1.67→1.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 12.4 / % possible all: 86.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YIB Resolution: 1.67→39.82 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.85 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→39.82 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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