+Open data
-Basic information
Entry | Database: PDB / ID: 7tqy | ||||||||||||
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Title | CaKip3[2-482] - ADP-AlFx in complex with a microtubule | ||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Kip3 / kinesin / motility / microtubule / tubulin | ||||||||||||
Function / homology | Function and homology information tubulin-dependent ATPase activity / plus-end specific microtubule depolymerization / regulation of mitotic spindle elongation / meiotic sister chromatid segregation / mitotic spindle astral microtubule / nuclear microtubule / mitotic spindle midzone / nuclear migration along microtubule / microtubule plus-end / mitotic spindle disassembly ...tubulin-dependent ATPase activity / plus-end specific microtubule depolymerization / regulation of mitotic spindle elongation / meiotic sister chromatid segregation / mitotic spindle astral microtubule / nuclear microtubule / mitotic spindle midzone / nuclear migration along microtubule / microtubule plus-end / mitotic spindle disassembly / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / plus-end-directed microtubule motor activity / Recruitment of NuMA to mitotic centrosomes / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / COPI-mediated anterograde transport / microtubule depolymerization / negative regulation of microtubule polymerization / kinesin complex / microtubule-based movement / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / mitotic spindle assembly / microtubule-based process / mitotic spindle organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Candida albicans (yeast) Sus scrofa (pig) | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.6 Å | ||||||||||||
Authors | Benoit, M.P.M.H. / Asenjo, A.B. / Hunter, B. / Allingham, J. / Sosa, H. | ||||||||||||
Funding support | United States, Canada, 3items
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Citation | Journal: Nat Commun / Year: 2022 Title: Kinesin-8-specific loop-2 controls the dual activities of the motor domain according to tubulin protofilament shape. Authors: Byron Hunter / Matthieu P M H Benoit / Ana B Asenjo / Caitlin Doubleday / Daria Trofimova / Corey Frazer / Irsa Shoukat / Hernando Sosa / John S Allingham / Abstract: Kinesin-8s are dual-activity motor proteins that can move processively on microtubules and depolymerize microtubule plus-ends, but their mechanism of combining these distinct activities remains ...Kinesin-8s are dual-activity motor proteins that can move processively on microtubules and depolymerize microtubule plus-ends, but their mechanism of combining these distinct activities remains unclear. We addressed this by obtaining cryo-EM structures (2.6-3.9 Å) of Candida albicans Kip3 in different catalytic states on the microtubule lattice and on a curved microtubule end mimic. We also determined a crystal structure of microtubule-unbound CaKip3-ADP (2.0 Å) and analyzed the biochemical activity of CaKip3 and kinesin-1 mutants. These data reveal that the microtubule depolymerization activity of kinesin-8 originates from conformational changes of its motor core that are amplified by dynamic contacts between its extended loop-2 and tubulin. On curved microtubule ends, loop-1 inserts into preceding motor domains, forming head-to-tail arrays of kinesin-8s that complement loop-2 contacts with curved tubulin and assist depolymerization. On straight tubulin protofilaments in the microtubule lattice, loop-2-tubulin contacts inhibit conformational changes in the motor core, but in the ADP-Pi state these contacts are relaxed, allowing neck-linker docking for motility. We propose that these tubulin shape-induced alternations between pro-microtubule-depolymerization and pro-motility kinesin states, regulated by loop-2, are the key to the dual activity of kinesin-8 motors. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tqy.cif.gz | 261.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tqy.ent.gz | 201.4 KB | Display | PDB format |
PDBx/mmJSON format | 7tqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/7tqy ftp://data.pdbj.org/pub/pdb/validation_reports/tq/7tqy | HTTPS FTP |
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-Related structure data
Related structure data | 26075MC 7lffC 7tqxC 7tqzC 7tr0C 7tr1C 7tr2C 7tr3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules KAB
#1: Protein | Mass: 54869.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: KIP3, orf19.7353, CAALFM_C305720CA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D8PKA4 |
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#2: Protein | Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / References: UniProt: Q2XVP4 |
#3: Protein | Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / References: UniProt: A0A287AGU7 |
-Non-polymers , 6 types, 7 molecules
#4: Chemical | ChemComp-AF3 / | ||||||
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#5: Chemical | ChemComp-ADP / | ||||||
#6: Chemical | #7: Chemical | ChemComp-GTP / | #8: Chemical | ChemComp-GDP / | #9: Chemical | ChemComp-TA1 / | |
-Details
Has ligand of interest | N |
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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 |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R2/2 | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 750 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 63.28 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 168.069 ° / Axial rise/subunit: 5.44 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Details: manual picking of filaments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255526 Details: 2 half datasets containing one distinct half of each filament were refined independently. Number of asymmetric units used is reported in "number of segments used", due to the local processing strategy employed. Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |