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Open data
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Basic information
Entry | Database: PDB / ID: 2wbe | ||||||
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Title | Kinesin-5-Tubulin Complex with AMPPNP | ||||||
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![]() | STRUCTURAL PROTEIN / EG5 / KLP61F / KINESIN / TUBULIN / MITOSIS / KINESIN-5 / GTP-BINDING / MOTOR PROTEIN / CELL DIVISION / CELL CYCLE / MICROTUBULE / ATP-BINDING / HOMOLOGY MODEL / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING | ||||||
Function / homology | ![]() aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / mitotic spindle microtubule / spindle elongation / positive regulation of Golgi to plasma membrane protein transport ...aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / mitotic spindle microtubule / spindle elongation / positive regulation of Golgi to plasma membrane protein transport / minus-end-directed microtubule motor activity / microtubule bundle formation / plus-end-directed microtubule motor activity / mitotic centrosome separation / positive regulation of axon guidance / microtubule associated complex / kinesin complex / microtubule-based movement / mitotic spindle pole / cytoskeletal motor activity / Golgi organization / microtubule-based process / protein secretion / mitotic spindle assembly / mitotic spindle organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / structural constituent of cytoskeleton / mitotic spindle / 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 / Golgi apparatus / endoplasmic reticulum / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9.4 Å | ||||||
![]() | Bodey, A.J. / Kikkawa, M. / Moores, C.A. | ||||||
![]() | ![]() Title: 9-Angström structure of a microtubule-bound mitotic motor. Authors: Andrew J Bodey / Masahide Kikkawa / Carolyn A Moores / ![]() Abstract: Kinesin-5 (K5) motors are important components of the microtubule (MT)-based cell division machinery and are targets for small-molecule inhibitors currently in cancer clinical trials. However, the ...Kinesin-5 (K5) motors are important components of the microtubule (MT)-based cell division machinery and are targets for small-molecule inhibitors currently in cancer clinical trials. However, the nature of the K5-MT interaction and the regulatory mechanisms that control it remain unclear. Using cryo-electron microscopy and image processing, we calculated the structure of a K5 motor bound to MTs at 9 A resolution, providing insight into this important interaction. Our reconstruction reveals the K5 motor domain in an ATP-like conformation in which MT binding induces the conserved nucleotide-sensing switch I and II loops to form a compact subdomain around the bound nucleotide. Our reconstruction also reveals a novel conformation for the K5-specific drug-binding loop 5, suggesting a possible role for it in switching K5s between force generation and diffusional modes of MT binding. Our data thus shed light on regulation of the interaction between spindle components important for chromosome segregation. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.7 KB | Display | ![]() |
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PDB format | ![]() | 190 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 60.7 KB | Display | |
Data in CIF | ![]() | 85 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1604MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 50107.238 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: 41911.566 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN WITH NECK LINKER, RESIDUES 1-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 6 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TA1.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TA1.gif)
![](data/chem/img/ANP.gif)
#4: Chemical | #5: Chemical | ChemComp-GTP / | #6: Chemical | ChemComp-GDP / | #7: Chemical | ChemComp-TA1 / | #8: Chemical | ChemComp-ANP / | |
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-Details
Nonpolymer details | PHOSPHOAMI |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: MICROTUBULE-KLP61F COMPLEX WITH AMPPNP / Type: COMPLEX |
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Buffer solution | Name: 80MM PIPES, 150MM NACL, 7MM MGCL2, 1MM EGTA, 1MM BETA-MERCAPTOETHANOL pH: 6.8 Details: 80MM PIPES, 150MM NACL, 7MM MGCL2, 1MM EGTA, 1MM BETA-MERCAPTOETHANOL |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Details: 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 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3940 nm / Nominal defocus min: 1080 nm / Cs: 2 mm |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 24 |
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Processing
EM software | Name: Ruby-Helix / Category: 3D reconstruction | ||||||||||||||||||||||||||||
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CTF correction | Details: PHASE FLIPPING, WIENER | ||||||||||||||||||||||||||||
3D reconstruction | Method: HELICAL PROCESSING / Resolution: 9.4 Å / Nominal pixel size: 1.4 Å / Actual pixel size: 1.4 Å Details: THE KLP61F HOMOLOGY MODEL WAS GENERATED WITH MODELLER 9V1 AND THE FOLLOWING TEMPLATES - 1MKJ.PDB, 1T5C.PDB AND 2KIN.PDB Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER Details: REFINEMENT PROTOCOL--HOMOLOGY (KLP61F), ELECTRON CRYSTALLOGRAPHY (TUBULIN) | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 9.4 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9.4 Å
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