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Yorodumi- PDB-3j6h: Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule -
+Open data
-Basic information
Entry | Database: PDB / ID: 3j6h | ||||||
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Title | Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/MOTOR PROTEIN / Kinesin / Motor domain / Rigor-conformation / Nucleotide-free kinesin / Microtubule / GMPCPP-microtubule / tubulin / Axonal transport / STRUCTURAL PROTEIN-MOTOR PROTEIN complex | ||||||
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 GTP to facilitate cellular and subcellular movement / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / neuron projection / GTPase activity / neuronal cell body / dendrite / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.1 Å | ||||||
Authors | Morikawa, M. / Yajima, H. / Nitta, R. / Inoue, S. / Ogura, T. / Sato, C. / 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j6h.cif.gz | 215.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j6h.ent.gz | 156 KB | Display | PDB format |
PDBx/mmJSON format | 3j6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j6h_validation.pdf.gz | 986.2 KB | Display | wwPDB validaton report |
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Full document | 3j6h_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3j6h_validation.xml.gz | 79.3 KB | Display | |
Data in CIF | 3j6h_validation.cif.gz | 106.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/3j6h ftp://data.pdbj.org/pub/pdb/validation_reports/j6/3j6h | HTTPS FTP |
-Related structure data
Related structure data | 5916MC 3wrdC 3x2tC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Protein , 3 types, 3 molecules ABK
#1: Protein | Mass: 48436.625 Da / Num. of mol.: 1 / Fragment: UNP residues 2-437 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: brain / References: UniProt: P02550 |
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#2: Protein | Mass: 47809.746 Da / Num. of mol.: 1 / Fragment: UNP residues 2-427 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: brain / References: UniProt: P02554 |
#3: Protein | Mass: 39615.137 Da / Num. of mol.: 1 / Fragment: UNP residues 1-345 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 |
-Non-polymers , 4 types, 5 molecules
#4: Chemical | #5: Chemical | ChemComp-GTP / | #6: Chemical | ChemComp-G2P / | #7: Chemical | ChemComp-SO4 / | |
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-Details
Sequence details | THIS SEQUENCE IS NATURAL VARIANT. |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Kinesin motor domain complexed with GMPCPP-microtubule Type: COMPLEX |
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Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: LEICA KF80 / Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL 2010F / Date: Jan 1, 2012 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 40000 X / Calibrated magnification: 40000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1200 nm / Cs: 3.3 mm |
Specimen holder | Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Each filament | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Method: Single Particle / Resolution: 8.1 Å / Num. of particles: 302000 / Nominal pixel size: 2.5 Å / Actual pixel size: 2.5 Å / Num. of class averages: 18 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Target criteria: Cross-correlation, Average map value, Atoms inside the contour Details: METHOD--Local refinement, Domain fitting REFINEMENT PROTOCOL--Rigid body refinement DETAILS--Initial local fitting was done using Chimera and for some loops Modeller was used. | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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