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Yorodumi- PDB-2zfk: Crystal Structure of the Kif1A Motor Domain during Mg release: Mg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zfk | ||||||
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Title | Crystal Structure of the Kif1A Motor Domain during Mg release: Mg-releasing Transition-2 | ||||||
Components | Kinesin-like protein KIF1A, Kinesin heavy chain isoform 5C | ||||||
Keywords | TRANSPORT PROTEIN / kinesin / Alpha and Beta Protein / Enzyme / ATPase / P-loop / Motor Protein / ATP-binding / Coiled coil / Microtubule / Nucleotide-binding | ||||||
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 / postsynaptic cytosol / ciliary rootlet / kinesin complex / synaptic vesicle transport / 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 / microtubule binding / postsynapse / microtubule / neuron projection / axon / dendrite / neuronal cell body / 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: 3.61 Å | ||||||
Authors | Nitta, R. / Okada, Y. / Hirokawa, N. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structural model for strain-dependent microtubule activation of Mg-ADP release from kinesin. Authors: Nitta, R. / 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 | 2zfk.cif.gz | 80.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zfk.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/2zfk ftp://data.pdbj.org/pub/pdb/validation_reports/zf/2zfk | HTTPS FTP |
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-Related structure data
Related structure data | 2zfiC 2zfjC 2zflC 2zfmC 1vfvS S: Starting model for refinement C: citing same article (ref.) |
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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: KIF1A (residues 1-355), KIF5C (residues 329-334) 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-ADP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 3235 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VFV Resolution: 3.61→14.99 Å / Rfactor Rfree error: 0.021 / Data cutoff high absF: 287001.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10.1994 Å2 / ksol: 0.09667957 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.61→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.6→3.82 Å / Rfactor Rfree error: 0.089 / Total num. of bins used: 6
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Xplor file |
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