+Open data
-Basic information
Entry | Database: PDB / ID: 2hxh | ||||||
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Title | KIF1A head-microtubule complex structure in adp-form | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / microtubule-based motor | ||||||
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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / synaptic vesicle / presynapse / mitotic cell cycle / microtubule binding / postsynapse / microtubule / hydrolase activity / neuron projection / axon / GTPase activity / neuronal cell body / dendrite / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 11 Å | ||||||
Authors | Kikkawa, M. / Hirokawa, N. | ||||||
Citation | Journal: EMBO J / Year: 2006 Title: High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations. Authors: Masahide Kikkawa / Nobutaka Hirokawa / Abstract: Kinesin is an ATP-driven microtubule (MT)-based motor fundamental to organelle transport. Although a number of kinesin crystal structures have been solved, the structural evidence for coupling ...Kinesin is an ATP-driven microtubule (MT)-based motor fundamental to organelle transport. Although a number of kinesin crystal structures have been solved, the structural evidence for coupling between the bound nucleotide and the conformation of kinesin is elusive. In addition, the structural basis of the MT-induced ATPase activity of kinesin is not clear because of the absence of the MT in the structure. Here, we report cryo-electron microscopy structures of the monomeric kinesin KIF1A-MT complex in two nucleotide states at about 10 A resolution, sufficient to reveal the secondary structure. These high-resolution maps visualized clear structural changes that suggest a mechanical pathway from the nucleotide to the neck linker via the motor core rotation. In addition, new nucleotide binding pocket conformations are observed that are different from X-ray crystallographic structures; it is closed in the 5'-adenylyl-imidodiphosphate state, but open in the ADP state. These results suggest a structural model of biased diffusion movement of monomeric kinesin motor. | ||||||
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 | 2hxh.cif.gz | 252.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hxh.ent.gz | 194.7 KB | Display | PDB format |
PDBx/mmJSON format | 2hxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hxh_validation.pdf.gz | 697.5 KB | Display | wwPDB validaton report |
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Full document | 2hxh_full_validation.pdf.gz | 817.1 KB | Display | |
Data in XML | 2hxh_validation.xml.gz | 41.2 KB | Display | |
Data in CIF | 2hxh_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/2hxh ftp://data.pdbj.org/pub/pdb/validation_reports/hx/2hxh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 50121.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550 |
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#2: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554 |
#3: Protein | Mass: 44302.855 Da / Num. of mol.: 1 / Fragment: KIF1A head domain / Mutation: P202A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: KIF1A / Plasmid: PET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33173 |
-Non-polymers , 5 types, 6 molecules
#4: Chemical | #5: Chemical | ChemComp-GTP / | #6: Chemical | ChemComp-GDP / | #7: Chemical | ChemComp-TA1 / | #8: Chemical | ChemComp-ADP / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: KIF1A head decorated-microtubule complex / Type: COMPLEX Details: SAMPLE DETAILS: TUBULIN WAS POLYMERIZED IN PEM BUFFER (PIPES 100 MM, PH 6.8, EGTA 1 MM, MGCL2, GTP 1MM, PACLITAXEL 10 MICRO M, 5% DMSO ) FOR 2 HRS AT 37C. A DROP OF THE POLYMERIZED ...Details: SAMPLE DETAILS: TUBULIN WAS POLYMERIZED IN PEM BUFFER (PIPES 100 MM, PH 6.8, EGTA 1 MM, MGCL2, GTP 1MM, PACLITAXEL 10 MICRO M, 5% DMSO ) FOR 2 HRS AT 37C. A DROP OF THE POLYMERIZED MICROTUBULE WAS PLACED ON THE HOLEY CARBON FILM ON THE EM-GRID AND LEFT FOR 10 S IN THE HUMID CHAMBER. THE MICROTUBULE SOLUTION WAS THEN ABSORBED BY FILTER PAPER, AND A DROP OF THE C351 SOLUTION (0.2 MG/ML) IN THE ASSAY BUFFER (IMIDAZOLE 50 MM, MG-ACETATE 5 MM, EGTA 1 MM, K-ACETATE 50 MM, DTT 10 MM, PACLITAXEL 10 MICRO M) WAS PUT ON THE GRID. IMMEDIATELY AFTER THE ABSORPTION OF THE DROP, THE GRID WAS PLUNGED INTO LIQUID ETHANE (-185C). |
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Buffer solution | Name: imidazole / pH: 7.4 / Details: imidazole |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Details: Ethan slash |
-Electron microscopy imaging
Microscopy | Model: JEOL 2010F / Date: Jan 1, 1999 |
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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: 33000 nm / Nominal defocus min: 11000 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 / Details: Scanned with LeafScan45 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: each filament | |||||||||||||||||||||
3D reconstruction | Method: Helical / Resolution: 11 Å / Nominal pixel size: 2.5 Å / Actual pixel size: 2.5 Å / Magnification calibration: Yes / Symmetry type: HELICAL | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Best cross-correlation / Details: REFINEMENT PROTOCOL--rigid body refinement | |||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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