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- PDB-4ck7: Pseudo-atomic model of microtubule-bound human kinesin-5 motor do... -
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Basic information
Entry | Database: PDB / ID: 4ck7 | ||||||
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Title | Pseudo-atomic model of microtubule-bound human kinesin-5 motor domain in presence of adp.alfx (NECK-LINKER IN ITS DISCONNECTED CONFORMATION, based on cryo-electron microscopy experiment | ||||||
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![]() | MOTOR PROTEIN / KINESINS / MICROTUBULES / MITOSIS / MECHANOCHEMISTRY | ||||||
Function / homology | ![]() spindle elongation / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / positive regulation of axon guidance / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / spindle organization ...spindle elongation / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / positive regulation of axon guidance / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / spindle organization / microtubule-based movement / microtubule-based process / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / mitotic spindle / structural constituent of cytoskeleton / spindle pole / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / nervous system development / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / protein heterodimerization activity / cell division / GTPase activity / GTP binding / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.2 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C | ||||||
![]() | Goulet, A. / Major, J. / Jun, Y. / Gross, S. / Rosenfeld, S. / Moores, C. | ||||||
![]() | ![]() Title: Comprehensive structural model of the mechanochemical cycle of a mitotic motor highlights molecular adaptations in the kinesin family. Authors: Adeline Goulet / Jennifer Major / Yonggun Jun / Steven P Gross / Steven S Rosenfeld / Carolyn A Moores / ![]() Abstract: Kinesins are responsible for a wide variety of microtubule-based, ATP-dependent functions. Their motor domain drives these activities, but the molecular adaptations that specify these diverse and ...Kinesins are responsible for a wide variety of microtubule-based, ATP-dependent functions. Their motor domain drives these activities, but the molecular adaptations that specify these diverse and essential cellular activities are poorly understood. It has been assumed that the first identified kinesin--the transport motor kinesin-1--is the mechanistic paradigm for the entire superfamily, but accumulating evidence suggests otherwise. To address the deficits in our understanding of the molecular basis of functional divergence within the kinesin superfamily, we studied kinesin-5s, which are essential mitotic motors whose inhibition blocks cell division. Using cryo-electron microscopy and determination of structure at subnanometer resolution, we have visualized conformations of microtubule-bound human kinesin-5 motor domain at successive steps in its ATPase cycle. After ATP hydrolysis, nucleotide-dependent conformational changes in the active site are allosterically propagated into rotations of the motor domain and uncurling of the drug-binding loop L5. In addition, the mechanical neck-linker element that is crucial for motor stepping undergoes discrete, ordered displacements. We also observed large reorientations of the motor N terminus that indicate its importance for kinesin-5 function through control of neck-linker conformation. A kinesin-5 mutant lacking this N terminus is enzymatically active, and ATP-dependent neck-linker movement and motility are defective, although not ablated. All these aspects of kinesin-5 mechanochemistry are distinct from kinesin-1. Our findings directly demonstrate the regulatory role of the kinesin-5 N terminus in collaboration with the motor's structured neck-linker and highlight the multiple adaptations within kinesin motor domains that tune their mechanochemistries according to distinct functional requirements. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 66.5 KB | Display | ![]() |
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PDB format | ![]() | 36.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2533MC ![]() 2534C ![]() 2535C ![]() 2536C ![]() 2537C ![]() 2538C ![]() 2539C ![]() 2540C ![]() 2541C ![]() 2542C ![]() 4ck5C ![]() 4ck6C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 50236.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 41673.105 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-367 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 6 types, 7 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TA1.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TA1.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/ADP.gif)
#4: Chemical | #5: Chemical | ChemComp-GTP / | #6: Chemical | ChemComp-GDP / | #7: Chemical | ChemComp-TA1 / | #8: Chemical | ChemComp-AF3 / | #9: Chemical | ChemComp-ADP / | |
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-Details
Sequence details | CYS-LITE MUTANT CONTAINING |
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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 |
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Sample preparation
Component | Name: MICROTUBULE-BOUND HUMAN KINESIN-5 MOTOR DOMAIN / Type: COMPLEX |
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Buffer solution | Name: 80 MM PIPES 5 MM MGCL2 1 MM EGTA 1 MM TCEP / pH: 6.8 / Details: 80 MM PIPES 5 MM MGCL2 1 MM EGTA 1 MM TCEP |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Mar 10, 2011 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2 mm |
Specimen holder | Temperature: 90 K |
Image recording | Electron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 125 |
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Processing
EM software |
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CTF correction | Details: FREALIGN | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 9.2 Å / Num. of particles: 10692 Details: THE N-TERMINAL SEQUENCE WAS MODELLED USING MODELLER. THE DISCONNECTED CONFORMATION OF THE NECK-LINKER WAS CALCULATED USING A CONJUGATE-GRADIENT ENERGY MINIMIZATION. SUBMISSION BASED ON ...Details: THE N-TERMINAL SEQUENCE WAS MODELLED USING MODELLER. THE DISCONNECTED CONFORMATION OF THE NECK-LINKER WAS CALCULATED USING A CONJUGATE-GRADIENT ENERGY MINIMIZATION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2533. (DEPOSITION ID: 12198). Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY | |||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 9.2 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9.2 Å
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