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- PDB-2zfj: Crystal Structure of the Kif1A Motor Domain during Mg release: Mg... -
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Basic information
Entry | Database: PDB / ID: 2zfj | ||||||
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Title | Crystal Structure of the Kif1A Motor Domain during Mg release: Mg-releasing Transition-1 | ||||||
![]() | Kinesin-like protein KIF1A, Kinesin heavy chain isoform 5C | ||||||
![]() | TRANSPORT PROTEIN / kinesin / Alpha and Beta Protein / Enzyme / ATPase / P-loop / Motor Protein / ATP-binding / Coiled coil / Microtubule / Nucleotide-binding | ||||||
Function / homology | ![]() 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 ...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 / plus-end-directed microtubule motor activity / motor neuron axon guidance / postsynaptic cytosol / ciliary rootlet / microtubule motor activity / kinesin complex / synaptic vesicle transport / 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 / mitotic cell cycle / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nitta, R. / Okada, Y. / Hirokawa, N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.2 KB | Display | ![]() |
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PDB format | ![]() | 56.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 717 KB | Display | ![]() |
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Full document | ![]() | 748.8 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zfiC ![]() 2zfkC ![]() 2zflC ![]() 2zfmC ![]() 1i5sS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.3 % |
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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 | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 3.2→50 Å / Num. obs: 4812 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1I5S Resolution: 3.2→19.96 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 120235.43 / 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: 58.06 Å2 / ksol: 0.291416 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
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Xplor file |
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