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- PDB-5hnx: Structural basis of backwards motion in kinesin-14: minus-end dir... -

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Basic information

Entry
Database: PDB / ID: 5hnx
TitleStructural basis of backwards motion in kinesin-14: minus-end directed nKn664 in the nucleotide-free state
Components
  • Protein claret segregational,kinesin-1/kinesin-14,Protein claret segregational
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsSTRUCTURAL PROTEIN/MOTOR PROTEIN / kinesin / kinesin-14 / microtubule / ATPase / STRUCTURAL PROTEIN-MOTOR PROTEIN complex
Function / homology
Function and homology information


minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / microtubule bundle formation / spindle assembly involved in female meiosis / regulation of mitotic spindle assembly ...minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / microtubule bundle formation / spindle assembly involved in female meiosis / regulation of mitotic spindle assembly / mitotic centrosome separation / positive regulation of axon guidance / meiotic spindle / minus-end-directed microtubule motor activity / spindle organization / mitotic spindle assembly / mRNA transport / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / mitotic spindle organization / chromosome segregation / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / microtubule cytoskeleton organization / spindle / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / cilium / protein heterodimerization activity / cell division / GTPase activity / ubiquitin protein ligase binding / centrosome / GTP binding / protein homodimerization activity / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. ...Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Protein claret segregational / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Rattus norvegicus (Norway rat)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsShigematsu, H. / Yokoyama, T. / Kikkawa, M. / Shirouzu, M. / Nitta, R.
CitationJournal: 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
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Other
Revision 1.3Nov 2, 2016Group: Other
Revision 1.4Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
K: Protein claret segregational,kinesin-1/kinesin-14,Protein claret segregational
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,4807
Polymers141,6353
Non-polymers1,8454
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9310 Å2
ΔGint-49 kcal/mol
Surface area43320 Å2

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Components

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Protein , 3 types, 3 molecules ABK

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50107.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856
#3: Protein Protein claret segregational,kinesin-1/kinesin-14,Protein claret segregational


Mass: 41620.250 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

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Non-polymers , 4 types, 4 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Minus-end directed Ncd chimera nKn664 in the AMPPNP state complexed with GDP-taxol microtubuleCOMPLEX#1-#30MULTIPLE SOURCES
2Tubulin alpha-1B chainCOMPLEX#11NATURAL
3Tubulin beta-2B chainCOMPLEX#21NATURAL
4Protein claret segregational,kinesin-1/kinesin-14,Protein claret segregationalCOMPLEX#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bos taurus (domestic cattle)9913
23Bos taurus (domestic cattle)9913
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDPlasmid
14Drosophila melanogaster (fruit fly)7227unknown
24Rattus norvegicus (Norway rat)10116unknown
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -25.725189 ° / Axial rise/subunit: 8.751208 Å / Axial symmetry: C1
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229516 / Details: High-resolution noise substitution was performed / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT

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