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Yorodumi- PDB-5hny: Structural basis of backwards motion in kinesin-14: plus-end dire... -
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-Basic information
Entry | Database: PDB / ID: 5hny | ||||||
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Title | Structural basis of backwards motion in kinesin-14: plus-end directed nKn669 in the AMPPNP state | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/MOTOR PROTEIN / kinesin / kinesin-14 / microtubule / ATPase / STRUCTURAL PROTEIN-MOTOR PROTEIN complex | ||||||
Function / homology | Function and homology information T=3 icosahedral viral capsid / positive regulation of axon guidance / microtubule-based process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / regulation of translation / mitotic cell cycle / nervous system development ...T=3 icosahedral viral capsid / positive regulation of axon guidance / microtubule-based process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / regulation of translation / mitotic cell cycle / nervous system development / microtubule / protein heterodimerization activity / GTPase activity / GTP binding / structural molecule activity / RNA binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) Rattus norvegicus (Norway rat) Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.3 Å | ||||||
Authors | Shigematsu, H. / Yokoyama, T. / Kikkawa, M. / Shirouzu, M. / Nitta, R. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility. Authors: Masahiko Yamagishi / Hideki Shigematsu / Takeshi Yokoyama / Masahide Kikkawa / Mitsuhiro Sugawa / Mari Aoki / Mikako Shirouzu / Junichiro Yajima / Ryo Nitta / Abstract: Kinesin-14 is a unique minus-end-directed microtubule-based motor. A swinging motion of a class-specific N-terminal neck helix has been proposed to produce minus-end directionality. However, it is ...Kinesin-14 is a unique minus-end-directed microtubule-based motor. A swinging motion of a class-specific N-terminal neck helix has been proposed to produce minus-end directionality. However, it is unclear how swinging of the neck helix is driven by ATP hydrolysis utilizing the highly conserved catalytic core among all kinesins. Here, using a motility assay, we show that in addition to the neck helix, the conserved five residues at the C-terminal region in kinesin-14, namely the neck mimic, are necessary to give kinesin-1 an ability to reverse its directionality toward the minus end of microtubules. Our structural analyses further demonstrate that the C-terminal neck mimic, in cooperation with conformational changes in the catalytic core during ATP binding, forms a kinesin-14 bundle with the N-terminal neck helix to swing toward the minus end of microtubules. Thus, the neck mimic plays a crucial role in coupling the chemical ATPase reaction with the mechanical cycle to produce the minus-end-directed motility of kinesin-14. | ||||||
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 | 5hny.cif.gz | 233.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hny.ent.gz | 187.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hny_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5hny_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5hny_validation.xml.gz | 57.8 KB | Display | |
Data in CIF | 5hny_validation.cif.gz | 80.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/5hny ftp://data.pdbj.org/pub/pdb/validation_reports/hn/5hny | HTTPS FTP |
-Related structure data
Related structure data | 8060MC 8058C 8059C 8061C 5hnwC 5hnxC 5hnzC 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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1 |
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-Components
-Protein , 3 types, 3 molecules ABK
#1: Protein | Mass: 48638.793 Da / Num. of mol.: 1 / Fragment: UNP residues 2-439 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947 |
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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) Bos taurus (cattle) / References: UniProt: Q6B856 |
#3: Protein | Mass: 41720.418 Da / Num. of mol.: 1 / Fragment: UNP residues 325-348, UNP residues 664-700 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Rattus norvegicus (Norway rat) Gene: ncd / Production host: Escherichia coli (E. coli) / References: UniProt: P20480 |
-Non-polymers , 5 types, 6 molecules
#4: Chemical | ChemComp-GTP / | ||||||
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#5: Chemical | #6: Chemical | ChemComp-GDP / | #7: Chemical | ChemComp-TA1 / | #8: Chemical | ChemComp-ANP / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
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Buffer solution | pH: 6.8 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: -25.725189 ° / Axial rise/subunit: 8.751208 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128254 / Details: High-resolution noise substitution was performed / Symmetry type: HELICAL |
Atomic model building | Protocol: FLEXIBLE FIT |