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Yorodumi- PDB-3wrd: Crystal Structure of the KIF5C Motor Domain Without Any Nucleotide -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wrd | ||||||
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Title | Crystal Structure of the KIF5C Motor Domain Without Any Nucleotide | ||||||
Components | Kinesin heavy chain isoform 5C | ||||||
Keywords | MOTOR PROTEIN / kinesin / motor domain / nucleotide-free / ATPase / nucleotide binding / microtubule / transport protein | ||||||
Function / homology | Function and homology information distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / motor neuron axon guidance / plus-end-directed microtubule motor activity / microtubule motor activity / ciliary rootlet ...distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / motor neuron axon guidance / plus-end-directed microtubule motor activity / microtubule motor activity / ciliary rootlet / kinesin complex / synaptic vesicle transport / postsynaptic cytosol / mRNA transport / axonal growth cone / axon cytoplasm / dendrite cytoplasm / axon guidance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / microtubule binding / microtubule / neuron projection / neuronal cell body / dendrite / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.86 Å | ||||||
Authors | Inoue, S. / Nitta, R. / Hirokawa, N. | ||||||
Citation | Journal: EMBO J / Year: 2015 Title: X-ray and Cryo-EM structures reveal mutual conformational changes of Kinesin and GTP-state microtubules upon binding. Authors: Manatsu Morikawa / Hiroaki Yajima / Ryo Nitta / Shigeyuki Inoue / Toshihiko Ogura / Chikara Sato / Nobutaka Hirokawa / Abstract: The molecular motor kinesin moves along microtubules using energy from ATP hydrolysis in an initial step coupled with ADP release. In neurons, kinesin-1/KIF5C preferentially binds to the GTP-state ...The molecular motor kinesin moves along microtubules using energy from ATP hydrolysis in an initial step coupled with ADP release. In neurons, kinesin-1/KIF5C preferentially binds to the GTP-state microtubules over GDP-state microtubules to selectively enter an axon among many processes; however, because the atomic structure of nucleotide-free KIF5C is unavailable, its molecular mechanism remains unresolved. Here, the crystal structure of nucleotide-free KIF5C and the cryo-electron microscopic structure of nucleotide-free KIF5C complexed with the GTP-state microtubule are presented. The structures illustrate mutual conformational changes induced by interaction between the GTP-state microtubule and KIF5C. KIF5C acquires the 'rigor conformation', where mobile switches I and II are stabilized through L11 and the initial portion of the neck-linker, facilitating effective ADP release and the weak-to-strong transition of KIF5C microtubule affinity. Conformational changes to tubulin strengthen the longitudinal contacts of the GTP-state microtubule in a similar manner to GDP-taxol microtubules. These results and functional analyses provide the molecular mechanism of the preferential binding of KIF5C to GTP-state microtubules. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wrd.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wrd.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 3wrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wrd_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 3wrd_full_validation.pdf.gz | 515.2 KB | Display | |
Data in XML | 3wrd_validation.xml.gz | 32 KB | Display | |
Data in CIF | 3wrd_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/3wrd ftp://data.pdbj.org/pub/pdb/validation_reports/wr/3wrd | HTTPS FTP |
-Related structure data
Related structure data | 5916C 3j6hC 3x2tC 2kinS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38255.551 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN, RESIDUES 1-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif5c / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28738 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.15 % / Mosaicity: 0.686 ° / Mosaicity esd: 0.008 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Ammonium sulfate, Sodium citrate, Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 21, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.86→50 Å / Num. all: 21497 / Num. obs: 21432 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.079 / Χ2: 0.889 / Net I/σ(I): 14.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2KIN Resolution: 2.86→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.324 / WRfactor Rwork: 0.254 / SU B: 0 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.845 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 228.46 Å2 / Biso mean: 102.294 Å2 / Biso min: 45.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.86→20 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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