+Open data
-Basic information
Entry | Database: PDB / ID: 5nd7 | ||||||||||||||||||||||||||||||||||||||||||
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Title | Microtubule-bound MKLP2 motor domain in the presence of AMPPNP | ||||||||||||||||||||||||||||||||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Kinesin Mitosis Microtubules | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information Mitotic Telophase/Cytokinesis / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation ...Mitotic Telophase/Cytokinesis / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases Activate Formins / Kinesins / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Aggrephagy / COPI-dependent Golgi-to-ER retrograde traffic / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / midbody abscission / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / MHC class II antigen presentation / microtubule bundle formation / positive regulation of axon guidance / microtubule motor activity / kinesin complex / intercellular bridge / microtubule-based movement / microtubule-based process / mitotic cytokinesis / regulation of cytokinesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / protein transport / mitotic cell cycle / nervous system development / midbody / microtubule binding / microtubule / hydrolase activity / protein heterodimerization activity / GTPase activity / GTP binding / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | Mus musculus (house mouse) Bos taurus (cattle) | ||||||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å | ||||||||||||||||||||||||||||||||||||||||||
Authors | Atherton, J. / Yu, I.-M. / Cook, A. / Muretta, J.M. / Joseph, A.P. / Major, J. / Sourigues, Y. / Clause, J. / Topf, M. / Rosenfeld, S.S. ...Atherton, J. / Yu, I.-M. / Cook, A. / Muretta, J.M. / Joseph, A.P. / Major, J. / Sourigues, Y. / Clause, J. / Topf, M. / Rosenfeld, S.S. / Houdusse, A. / Moores, C.A. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | United Kingdom, United States, 13items
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Citation | Journal: Elife / Year: 2017 Title: The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry. Authors: Joseph Atherton / I-Mei Yu / Alexander Cook / Joseph M Muretta / Agnel Joseph / Jennifer Major / Yannick Sourigues / Jeffrey Clause / Maya Topf / Steven S Rosenfeld / Anne Houdusse / Carolyn A Moores / Abstract: MKLP2, a kinesin-6, has critical roles during the metaphase-anaphase transition and cytokinesis. Its motor domain contains conserved nucleotide binding motifs, but is divergent in sequence (~35% ...MKLP2, a kinesin-6, has critical roles during the metaphase-anaphase transition and cytokinesis. Its motor domain contains conserved nucleotide binding motifs, but is divergent in sequence (~35% identity) and size (~40% larger) compared to other kinesins. Using cryo-electron microscopy and biophysical assays, we have undertaken a mechanochemical dissection of the microtubule-bound MKLP2 motor domain during its ATPase cycle, and show that many facets of its mechanism are distinct from other kinesins. While the MKLP2 neck-linker is directed towards the microtubule plus-end in an ATP-like state, it does not fully dock along the motor domain. Furthermore, the footprint of the MKLP2 motor domain on the MT surface is altered compared to motile kinesins, and enhanced by kinesin-6-specific sequences. The conformation of the highly extended loop6 insertion characteristic of kinesin-6s is nucleotide-independent and does not contact the MT surface. Our results emphasize the role of family-specific insertions in modulating kinesin motor function. | ||||||||||||||||||||||||||||||||||||||||||
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 | 5nd7.cif.gz | 939.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nd7.ent.gz | 800.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nd7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5nd7_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5nd7_validation.xml.gz | 152.5 KB | Display | |
Data in CIF | 5nd7_validation.cif.gz | 211 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/5nd7 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5nd7 | HTTPS FTP |
-Related structure data
Related structure data | 3623MC 3620C 3621C 3622C 5nd2C 5nd3C 5nd4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Number of models | 5 |
-Components
-Protein , 3 types, 3 molecules CAB
#1: Protein | Mass: 56021.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif20a, Rab6kifl / Production host: Escherichia coli (E. coli) / References: UniProt: P97329 |
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#2: Protein | Mass: 50107.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F2Z4C1, UniProt: P81947*PLUS |
#3: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 |
-Non-polymers , 5 types, 6 molecules
#4: Chemical | #5: Chemical | ChemComp-ANP / | #6: Chemical | ChemComp-GTP / | #7: Chemical | ChemComp-GDP / | #8: Chemical | ChemComp-TA1 / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10858 Details: Gold-standard FSCtrue using noise substitution test (Chen et al., 2014) Symmetry type: POINT |