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Yorodumi- PDB-1i5s: CRYSTAL STRUCTURE OF THE KIF1A MOTOR DOMAIN COMPLEXED WITH MG-ADP -
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-Basic information
Entry | Database: PDB / ID: 1i5s | ||||||
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Title | CRYSTAL STRUCTURE OF THE KIF1A MOTOR DOMAIN COMPLEXED WITH MG-ADP | ||||||
Components | KINESIN-LIKE PROTEIN KIF1A | ||||||
Keywords | TRANSPORT PROTEIN / kinesin catalytic core / motor domain | ||||||
Function / homology | Function and homology information anterograde synaptic vesicle transport / protein transport along microtubule / interkinetic nuclear migration / neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / Kinesins / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / regulation of dendritic spine development ...anterograde synaptic vesicle transport / protein transport along microtubule / interkinetic nuclear migration / neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / Kinesins / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / regulation of dendritic spine development / 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 / vesicle-mediated transport / axon cytoplasm / 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 Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kikkawa, M. / Sablin, E.P. / Okada, Y. / Yajima, H. / Fletterick, R.J. / Hirokawa, N. | ||||||
Citation | Journal: Nature / Year: 2001 Title: Switch-based mechanism of kinesin motors. Authors: M Kikkawa / E P Sablin / Y Okada / H Yajima / R J Fletterick / N Hirokawa / Abstract: Kinesin motors are specialized enzymes that use hydrolysis of ATP to generate force and movement along their cellular tracks, the microtubules. Although numerous biochemical and biophysical studies ...Kinesin motors are specialized enzymes that use hydrolysis of ATP to generate force and movement along their cellular tracks, the microtubules. Although numerous biochemical and biophysical studies have accumulated much data that link microtubule-assisted ATP hydrolysis to kinesin motion, the structural view of kinesin movement remains unclear. This study of the monomeric kinesin motor KIF1A combines X-ray crystallography and cryo-electron microscopy, and allows analysis of force-generating conformational changes at atomic resolution. The motor is revealed in its two functionally critical states-complexed with ADP and with a non-hydrolysable analogue of ATP. The conformational change observed between the ADP-bound and the ATP-like structures of the KIF1A catalytic core is modular, extends to all kinesins and is similar to the conformational change used by myosin motors and G proteins. Docking of the ADP-bound and ATP-like crystallographic models of KIF1A into the corresponding cryo-electron microscopy maps suggests a rationale for the plus-end directional bias associated with the kinesin catalytic core. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 1i5s.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i5s.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 1i5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i5s_validation.pdf.gz | 736.4 KB | Display | wwPDB validaton report |
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Full document | 1i5s_full_validation.pdf.gz | 748.2 KB | Display | |
Data in XML | 1i5s_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 1i5s_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/1i5s ftp://data.pdbj.org/pub/pdb/validation_reports/i5/1i5s | HTTPS FTP |
-Related 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: 41240.324 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN / Mutation: P202A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: KIFA / Plasmid: PET21B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33173 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#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: 2.1 Å3/Da / Density % sol: 38.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4000, 100mM Tris-HCl pH 8.5, 200mM sodium acetate, 8% (w/v) sucrose, 4mM MgCl2, 10mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 30, 2000 / Details: mirrors |
Radiation | Monochromator: Cyclindrically bent cubed root Si(311), asymmetric cut, horizontal focus Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. all: 18095 / Num. obs: 17751 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 7.3 / Num. unique all: 1760 / Rsym value: 0.147 / % possible all: 96.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: catalytic core of the conventional rat kinesin Resolution: 2.2→19.76 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 818766.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: MLI
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.61 Å2 / ksol: 0.392 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.258 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.252 |