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Yorodumi- PDB-7eob: Crystal structure of KIF1A Motor-Neck domain E239K mutant with AD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eob | ||||||||||||||||||
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Title | Crystal structure of KIF1A Motor-Neck domain E239K mutant with ADP-Mg-AlFx | ||||||||||||||||||
Components | Kinesin-like protein KIF1A | ||||||||||||||||||
Keywords | MOTOR PROTEIN / kinesin | ||||||||||||||||||
Function / homology | Function and homology information protein transport along microtubule / neuronal dense core vesicle membrane / interkinetic nuclear migration / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / Kinesins / regulation of dendritic spine development / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport ...protein transport along microtubule / neuronal dense core vesicle membrane / interkinetic nuclear migration / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / Kinesins / regulation of dendritic spine development / 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 / kinesin complex / microtubule-based movement / neuronal dense core vesicle / axon cytoplasm / vesicle-mediated transport / 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 Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||||||||||||||
Authors | Ogawa, T. / Jiang, X. / Hirokawa, N. | ||||||||||||||||||
Funding support | Japan, 5items
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Citation | Journal: Embo J. / Year: 2022 Title: A neuropathy-associated kinesin KIF1A mutation hyper-stabilizes the motor-neck interaction during the ATPase cycle. Authors: Morikawa, M. / Jerath, N.U. / Ogawa, T. / Morikawa, M. / Tanaka, Y. / Shy, M.E. / Zuchner, S. / Hirokawa, N. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eob.cif.gz | 154.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eob.ent.gz | 117.7 KB | Display | PDB format |
PDBx/mmJSON format | 7eob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/7eob ftp://data.pdbj.org/pub/pdb/validation_reports/eo/7eob | HTTPS FTP |
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-Related structure data
Related structure data | 7eo9SC 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: 43972.543 Da / Num. of mol.: 1 / Mutation: E239K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif1a, Atsv, Kif1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33173 |
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#2: Chemical | ChemComp-AF3 / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ADP / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Ammonium acetate, Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→30 Å / Num. obs: 36686 / % possible obs: 97.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.04 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3095 / CC1/2: 0.805 / Rpim(I) all: 0.376 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EO9 Resolution: 1.76→30 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 107.82 Å2 / Biso mean: 40.2319 Å2 / Biso min: 20.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.763→1.808 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.8417 Å / Origin y: 3.311 Å / Origin z: 19.3472 Å
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