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Yorodumi- PDB-1vfv: Crystal Structure of the Kif1A Motor Domain Complexed With Mg-AMPPNP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vfv | ||||||
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Title | Crystal Structure of the Kif1A Motor Domain Complexed With Mg-AMPPNP | ||||||
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 anterograde synaptic vesicle transport / distal axon / protein transport along microtubule / anterograde dendritic transport of messenger ribonucleoprotein complex / interkinetic nuclear migration / neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde dendritic transport of neurotransmitter receptor complex / Kinesins / anterograde neuronal dense core vesicle transport ...anterograde synaptic vesicle transport / distal axon / protein transport along microtubule / anterograde dendritic transport of messenger ribonucleoprotein complex / interkinetic nuclear migration / neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde dendritic transport of neurotransmitter receptor complex / Kinesins / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / apolipoprotein receptor binding / COPI-dependent Golgi-to-ER retrograde traffic / regulation of dendritic spine development / intracellular mRNA localization / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / motor neuron axon guidance / plus-end-directed microtubule motor activity / microtubule motor activity / ciliary rootlet / kinesin complex / synaptic vesicle transport / postsynaptic cytosol / microtubule-based movement / neuronal dense core vesicle / mRNA transport / axonal growth cone / vesicle-mediated transport / axon cytoplasm / dendrite cytoplasm / axon guidance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / synaptic vesicle / presynapse / microtubule binding / postsynapse / 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: 1.85 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 | 1vfv.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vfv.ent.gz | 62.2 KB | Display | PDB format |
PDBx/mmJSON format | 1vfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vfv_validation.pdf.gz | 782.6 KB | Display | wwPDB validaton report |
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Full document | 1vfv_full_validation.pdf.gz | 797.1 KB | Display | |
Data in XML | 1vfv_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 1vfv_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/1vfv ftp://data.pdbj.org/pub/pdb/validation_reports/vf/1vfv | HTTPS FTP |
-Related structure data
Related structure data | 1vfwC 1vfxC 1vfzC 1i6iS 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: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: P33173, UniProt: P28738 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ANP / |
#4: 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: 2.32 Å3/Da / Density % sol: 46.99 % |
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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: APS / Beamline: 19-ID / Wavelength: 1.03 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Jul 27, 2002 |
Radiation | Monochromator: DOUBLE CRYSTAL SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 32645 / Num. obs: 32188 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.5 Å2 |
Reflection shell | Resolution: 1.85→1.92 Å / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I6I Resolution: 1.85→23.17 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 731326.02 / 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: 61.7557 Å2 / ksol: 0.376522 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→23.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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