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- PDB-4aqw: Model of human kinesin-5 motor domain (1II6, 3HQD) and mammalian ... -
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Basic information
Entry | Database: PDB / ID: 4aqw | ||||||
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Title | Model of human kinesin-5 motor domain (1II6, 3HQD) and mammalian tubulin heterodimer (1JFF) docked into the 9.5-angstrom cryo-EM map of microtubule-bound kinesin-5 motor domain in the rigor state. | ||||||
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![]() | MOTOR PROTEIN / MICROTUBULE / MITOSIS / CANCER | ||||||
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 / structural constituent of cytoskeleton / mitotic spindle / spindle pole / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / mitotic cell cycle / nervous system development / 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: 9.5 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C | ||||||
![]() | Goulet, A. / Behnke-Parks, W.M. / Sindelar, C.V. / Rosenfeld, S.S. / Moores, C.A. | ||||||
![]() | ![]() Title: The structural basis of force generation by the mitotic motor kinesin-5. Authors: Adeline Goulet / William M Behnke-Parks / Charles V Sindelar / Jennifer Major / Steven S Rosenfeld / Carolyn A Moores / ![]() Abstract: Kinesin-5 is required for forming the bipolar spindle during mitosis. Its motor domain, which contains nucleotide and microtubule binding sites and mechanical elements to generate force, has evolved ...Kinesin-5 is required for forming the bipolar spindle during mitosis. Its motor domain, which contains nucleotide and microtubule binding sites and mechanical elements to generate force, has evolved distinct properties for its spindle-based functions. In this study, we report subnanometer resolution cryoelectron microscopy reconstructions of microtubule-bound human kinesin-5 before and after nucleotide binding and combine this information with studies of the kinetics of nucleotide-induced neck linker and cover strand movement. These studies reveal coupled, nucleotide-dependent conformational changes that explain many of this motor's properties. We find that ATP binding induces a ratchet-like docking of the neck linker and simultaneous, parallel docking of the N-terminal cover strand. Loop L5, the binding site for allosteric inhibitors of kinesin-5, also undergoes a dramatic reorientation when ATP binds, suggesting that it is directly involved in controlling nucleotide binding. Our structures indicate that allosteric inhibitors of human kinesin-5, which are being developed as anti-cancer therapeutics, bind to a motor conformation that occurs in the course of normal function. However, due to evolutionarily defined sequence variations in L5, this conformation is not adopted by invertebrate kinesin-5s, explaining their resistance to drug inhibition. Together, our data reveal the precision with which the molecular mechanism of kinesin-5 motors has evolved for force generation. | ||||||
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 | ![]() | 66.1 KB | Display | ![]() |
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PDB format | ![]() | 35.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 31.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2078MC ![]() 2077C ![]() 2079C ![]() 2080C ![]() 2081C ![]() 2152C ![]() 4aqvC ![]() 4a2t 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 , 4 types, 4 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TA1.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TA1.gif)
#4: Chemical | ChemComp-GTP / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-GDP / |
#7: Chemical | ChemComp-TA1 / |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN C, CYS 25 TO VAL ENGINEERED RESIDUE IN CHAIN C, CYS 43 TO SER ...ENGINEERED |
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Sequence details | CYS-LIGHT CONSTRUCT (C25V,C43S,C87A,C99A). THE MUTATION T126C WAS INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 13-PROTOFILAMENT MICROTUBULE-BOUND HUMAN KINESIN-5 MOTOR DOMAIN IN ABSENCE OF NUCLEOTIDES Type: COMPLEX |
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Buffer solution | Name: 80 MM PIPES, 5 MM MGCL2, 1 MM EGTA, 1 U/ML APYRASE / pH: 6.8 / Details: 80 MM PIPES, 5 MM MGCL2, 1 MM EGTA, 1 U/ML APYRASE |
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 16, 2011 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2300 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: 138 |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: FREALIGN | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 9.5 Å / Num. of particles: 6748 / Nominal pixel size: 2.8 Å Details: THE LOOP 5 (119-131) WAS MODELED WITH MODELLER. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2078. (DEPOSITION ID: 10752). Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--RIGID BODY (1JFF). RIGID BODY AND FLEXIBLE FITTING FOR THE CHIMERIC MODEL BUILT USING 1II6 AND 3HQD. REFINEMENT PROTOCOL--X-RAY | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 9.5 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9.5 Å
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