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Yorodumi- PDB-4ck5: Pseudo-atomic model of microtubule-bound human kinesin-5 motor do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ck5 | ||||||
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Title | Pseudo-atomic model of microtubule-bound human kinesin-5 motor domain in the ADP state, based on cryo-electron microscopy experiment. | ||||||
Components |
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Keywords | MOTOR PROTEIN / KINESINS / MICROTUBULES / MITOSIS / MECHANOCHEMISTRY | ||||||
Function / homology | Function and homology information 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 | HOMO SAPIENS (human) BOS TAURUS (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C | ||||||
Authors | Goulet, A. / Major, J. / Jun, Y. / Gross, S. / Rosenfeld, S. / Moores, C. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2014 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4ck5.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ck5.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ck5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ck5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4ck5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ck5_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 4ck5_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/4ck5 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/4ck5 | HTTPS FTP |
-Related structure data
Related structure data | 2537MC 2533C 2534C 2535C 2536C 2538C 2539C 2540C 2541C 2542C 4ck6C 4ck7C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-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) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: Q2HJ86 |
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#2: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: Q6B856 |
#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.) HOMO SAPIENS (human) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P52732 |
-Non-polymers , 5 types, 5 molecules
#4: Chemical | ChemComp-GTP / |
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#5: Chemical | ChemComp-GDP / |
#6: Chemical | ChemComp-TA1 / |
#7: Chemical | ChemComp-MG / |
#8: Chemical | ChemComp-ADP / |
-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 |
-Sample preparation
Component | Name: microtubule-bound human kinesin-5 motor domain in the ADP state Type: COMPLEX Details: 13-PROTOFILAMENT MICROTUBULE- BOUND HUMAN KINESIN-5 MOTOR DOMAIN IN PRESENCE OF ADP |
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Buffer solution | Name: 20 MM PIPES, 5 MM MGCL2, 1 MM EGTA, 10 MM ADP / pH: 6.8 / Details: 20 MM PIPES, 5 MM MGCL2, 1 MM EGTA, 10 MM ADP |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Oct 20, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 68000 X / Nominal defocus max: 2400 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: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 160 |
-Processing
EM software |
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CTF correction | Details: FREALIGN | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 10 Å / Num. of particles: 9615 / Actual pixel size: 2.2 Å Details: TO ACCOUNT FOR THE FACT THAT HELIX ALPHA4 IS LONGER IN OUR RECONSTRUCTION THAN IN THE AVAILABLE ADP CRYSTAL STRUCTURES, WE MODELLED 7 HELICAL TURNS OF HELIX ALPHA4 ( RESIDUES D279-E304), AS ...Details: TO ACCOUNT FOR THE FACT THAT HELIX ALPHA4 IS LONGER IN OUR RECONSTRUCTION THAN IN THE AVAILABLE ADP CRYSTAL STRUCTURES, WE MODELLED 7 HELICAL TURNS OF HELIX ALPHA4 ( RESIDUES D279-E304), AS OBSERVED IN THE ENTRY 3HQD. THE N- TERMINAL SEQUENCE WAS MODELLED USING MODELLER. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2537. (DEPOSITION ID: 12202). Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--FLEXIBLE | |||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 10 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 10 Å
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