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Yorodumi- PDB-5jvr: The neck-linker of Mus musculus KIF3A fused to the alpha 7 helix ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jvr | ||||||
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Title | The neck-linker of Mus musculus KIF3A fused to the alpha 7 helix of Drosophila melanogaster Kinesin-1 fused to EB1 | ||||||
Components | Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1 | ||||||
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 / actin filament bundle organization / anterograde axonal transport of mitochondrion / anterograde dendritic transport / ovarian nurse cell to oocyte transport / intraciliary transport particle B binding / mitochondrion distribution ...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 / actin filament bundle organization / anterograde axonal transport of mitochondrion / anterograde dendritic transport / ovarian nurse cell to oocyte transport / intraciliary transport particle B binding / mitochondrion distribution / alpha-tubulin acetylation / larval locomotory behavior / oocyte microtubule cytoskeleton polarization / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / Activation of SMO / pole plasm oskar mRNA localization / Intraflagellar transport / oocyte dorsal/ventral axis specification / centriole-centriole cohesion / pole plasm assembly / protein localization to astral microtubule / microtubule sliding / dorsal appendage formation / cortical microtubule cytoskeleton / microtubule anchoring at centrosome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / transport along microtubule / larval somatic muscle development / centrosome separation / mitotic spindle astral microtubule end / positive regulation of keratinocyte proliferation / anterograde dendritic transport of neurotransmitter receptor complex / Kinesins / protein localization to cell junction / cilium movement / ribbon synapse / motile cilium assembly / photoreceptor connecting cilium / actin cap / protein localization to microtubule / inner ear receptor cell stereocilium organization / COPI-dependent Golgi-to-ER retrograde traffic / Hedgehog 'off' state / dorsal/ventral neural tube patterning / microtubule plus-end / cell projection membrane / positive regulation of intracellular protein transport / dentate gyrus development / attachment of mitotic spindle microtubules to kinetochore / MHC class II antigen presentation / non-motile cilium assembly / microtubule bundle formation / microtubule plus-end binding / anterograde axonal transport / neural precursor cell proliferation / dorsal/ventral pattern formation / axo-dendritic transport / plus-end-directed microtubule motor activity / motile cilium / nuclear migration / stress granule disassembly / determination of left/right symmetry / protein localization to centrosome / dendrite morphogenesis / neural tube development / anterior/posterior pattern specification / microtubule organizing center / microtubule motor activity / negative regulation of microtubule polymerization / kinesin complex / smoothened signaling pathway / synaptic vesicle transport / spectrin binding / intracellular distribution of mitochondria / tropomyosin binding / microtubule-based movement / heart looping / mitotic spindle pole / cytoskeletal motor activity / microtubule polymerization / cytoplasmic microtubule / axoneme / establishment of mitotic spindle orientation / kinesin binding / keratinocyte proliferation / cilium assembly / epidermis development / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / forebrain development / axon cytoplasm / Recruitment of mitotic centrosome proteins and complexes Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Drosophila melanogaster (fruit fly) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 5jvr.cif.gz | 238.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jvr.ent.gz | 196.1 KB | Display | PDB format |
PDBx/mmJSON format | 5jvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jvr_validation.pdf.gz | 478.7 KB | Display | wwPDB validaton report |
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Full document | 5jvr_full_validation.pdf.gz | 482 KB | Display | |
Data in XML | 5jvr_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 5jvr_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/5jvr ftp://data.pdbj.org/pub/pdb/validation_reports/jv/5jvr | HTTPS FTP |
-Related structure data
Related structure data | 5jv3C 5jvmC 5jvpC 5jvsC 5jvuC 5jx1C 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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Unit cell |
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-Components
#1: Protein | Mass: 8987.933 Da / Num. of mol.: 8 Fragment: UNP P28741 residues 352-359,UNP P17210 residues 345-358,UNP Q15691 residues 207-257 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Homo sapiens (human) Gene: Kif3a, Kif3, Khc, kin, CG7765, MAPRE1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P28741, UniProt: P17210, UniProt: Q15691 #2: 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: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 32% (w/v) polyethylene glycol dimethyl ether (DMPEG) 500, 30 mM MgCl2, 10 mM diethylenetriamine, 100 mM sodium 3-[4-(2-Hydroxyethyl)-1-piperazinyl]propanesulfonic acid (HEPPS) pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.88 Å / Num. obs: 52346 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 31.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 3.2 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YIB Resolution: 2.1→43.88 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.44 / 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: 2.1→43.88 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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