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Yorodumi- PDB-7tr1: CaKip3[2-436]-L2-mutant(HsKHC) - AMP-PNP in complex with a microtubule -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tr1 | ||||||||||||
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Title | CaKip3[2-436]-L2-mutant(HsKHC) - AMP-PNP in complex with a microtubule | ||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Kip3 / kinesin / motility / microtubule / tubulin | ||||||||||||
Function / homology | Function and homology information cytoplasm organization / cytolytic granule membrane / mitotic spindle astral microtubule / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / mitotic spindle midzone / retrograde neuronal dense core vesicle transport ...cytoplasm organization / cytolytic granule membrane / mitotic spindle astral microtubule / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / mitotic spindle midzone / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / natural killer cell mediated cytotoxicity / 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 / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / plus-end-directed microtubule motor activity / Kinesins / RHO GTPases activate KTN1 / RHO GTPases activate IQGAPs / stress granule disassembly / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / mitochondrion transport along microtubule / microtubule depolymerization / ciliary rootlet / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / centrosome localization / microtubule motor activity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / mitotic sister chromatid segregation / centriolar satellite / axon cytoplasm / phagocytic vesicle / MHC class II antigen presentation / dendrite cytoplasm / regulation of membrane potential / axon guidance / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / cellular response to type II interferon / microtubule cytoskeleton organization / microtubule cytoskeleton / Signaling by ALK fusions and activated point mutants / mitotic cell cycle / microtubule binding / vesicle / microtubule / cadherin binding / GTPase activity / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Candida albicans (yeast) Homo sapiens (human) Sus scrofa (pig) | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Benoit, M.P.M.H. / Asenjo, A.B. / Hunter, B. / Allingham, J.S. / 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 | 7tr1.cif.gz | 256.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tr1.ent.gz | 197.9 KB | Display | PDB format |
PDBx/mmJSON format | 7tr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tr1_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7tr1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7tr1_validation.xml.gz | 50.6 KB | Display | |
Data in CIF | 7tr1_validation.cif.gz | 73.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/7tr1 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/7tr1 | HTTPS FTP |
-Related structure data
Related structure data | 26078MC 7lffC 7tqxC 7tqyC 7tqzC 7tr0C 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: 46344.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 2-436 of CaKip, with L2 swapped with the one of HsKHC Source: (gene. exp.) Candida albicans (yeast), (gene. exp.) Homo sapiens (human) Gene: CAWG_02882, KIF5B, KNS, KNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: C4YNU9, UniProt: P33176 |
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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 , 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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-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 FIELD / Nominal defocus max: 1750 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 64 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 168.084 ° / Axial rise/subunit: 5.54 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Details: manual picking of filaments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67238 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 |