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Yorodumi- PDB-1vfz: Crystal Structure of the Kif1A Motor Domain Complexed With ADP-Mg-VO4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vfz | ||||||
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Title | Crystal Structure of the Kif1A Motor Domain Complexed With ADP-Mg-VO4 | ||||||
Components | PROTEIN (Fusion protein consisting of Kinesin-like protein KIF1A, Kinesin heavy chain isoform 5C and A HIS TAG | ||||||
Keywords | TRANSPORT PROTEIN / kinesin / microtubule / motor | ||||||
Function / homology | Function and homology information distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / protein transport along microtubule / neuronal dense core vesicle membrane / interkinetic nuclear migration / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / anterograde dendritic transport of neurotransmitter receptor complex / retrograde neuronal dense core vesicle transport / Kinesins ...distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / protein transport along microtubule / neuronal dense core vesicle membrane / interkinetic nuclear migration / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / anterograde dendritic transport of neurotransmitter receptor complex / retrograde neuronal dense core vesicle transport / Kinesins / regulation of dendritic spine development / anterograde axonal protein transport / intracellular mRNA localization / apolipoprotein receptor binding / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / plus-end-directed microtubule motor activity / motor neuron axon guidance / ciliary rootlet / postsynaptic cytosol / synaptic vesicle transport / kinesin complex / microtubule motor activity / microtubule-based movement / neuronal dense core vesicle / mRNA transport / axonal growth cone / axon cytoplasm / vesicle-mediated transport / dendrite cytoplasm / axon guidance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / synaptic vesicle / presynapse / postsynapse / microtubule binding / microtubule / neuron projection / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Nitta, R. / Kikkawa, M. / Okada, Y. / Hirokawa, N. | ||||||
Citation | Journal: Science / Year: 2004 Title: KIF1A Alternately Uses Two Loops to Bind Microtubules Authors: Nitta, R. / Kikkawa, M. / Okada, Y. / Hirokawa, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vfz.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vfz.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 1vfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/1vfz ftp://data.pdbj.org/pub/pdb/validation_reports/vf/1vfz | HTTPS FTP |
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-Related structure data
Related structure data | 1vfvC 1vfwC 1vfxC 1i5sS 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
#1: Protein | Mass: 41128.215 Da / Num. of mol.: 1 Fragment: Motor Domain OF Kinesin-like protein KIF1A and RESIDUES 329-334 OF Kinesin heavy chain isoform 5C Source method: isolated from a genetically manipulated source Details: FUSION PROTEIN COMPRISES RESIDUES 1-355 OF Kinesin-like protein KIF1A, AND RESIDUES 329-334 OF Kinesin heavy chain isoform 5C, AND C-TERMINAL TAIL WITH SEQUENCE HHHHH Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / References: UniProt: P33173, UniProt: P28738 |
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#2: Chemical | ChemComp-VO4 / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ADP / |
#5: 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: 2.12 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, Sodium acetate, Tris-HCl, Xylitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2003 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. all: 17233 / Num. obs: 17147 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.2 Å2 |
Reflection shell | Resolution: 2.24→2.32 Å / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I5S Resolution: 2.24→23.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 101547.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.1818 Å2 / ksol: 0.420953 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.24→23.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.38 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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