+Open data
-Basic information
Entry | Database: PDB / ID: 6zph | |||||||||||||||||||||
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Title | Kinesin binding protein complexed with Kif15 motor domain | |||||||||||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Kinesin / microtubules / kinesin binding protein / KBP | |||||||||||||||||||||
Function / homology | Function and homology information plus-end kinesin complex / central nervous system projection neuron axonogenesis / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / mitochondrial transport / microtubule-based movement / cytoskeletal motor activity / kinesin binding ...plus-end kinesin complex / central nervous system projection neuron axonogenesis / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / mitochondrial transport / microtubule-based movement / cytoskeletal motor activity / kinesin binding / neuron projection maintenance / MHC class II antigen presentation / microtubule cytoskeleton organization / spindle / mitotic cell cycle / microtubule binding / in utero embryonic development / microtubule / cytoskeleton / centrosome / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 Å | |||||||||||||||||||||
Authors | Atherton, J. / Hummel, J.J.A. / Olieric, N. / Locke, J. / Pena, A. / Rosenfeld, S.S. / Steinmetz, M.O. / Hoogenraad, C.C. / Moores, C.A. | |||||||||||||||||||||
Funding support | United Kingdom, Switzerland, United States, 6items
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Citation | Journal: Elife / Year: 2020 Title: The mechanism of kinesin inhibition by kinesin-binding protein. Authors: Joseph Atherton / Jessica Ja Hummel / Natacha Olieric / Julia Locke / Alejandro Peña / Steven S Rosenfeld / Michel O Steinmetz / Casper C Hoogenraad / Carolyn A Moores / Abstract: Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of ...Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of intracellular cargo distribution. Kinesin-binding protein (KBP) interacts with a subset of kinesins via their motor domains, inhibits their microtubule (MT) attachment, and blocks their cellular function. However, its mechanisms of inhibition and selectivity have been unclear. Here we use cryo-electron microscopy to reveal the structure of KBP and of a KBP-kinesin motor domain complex. KBP is a tetratricopeptide repeat-containing, right-handed α-solenoid that sequesters the kinesin motor domain's tubulin-binding surface, structurally distorting the motor domain and sterically blocking its MT attachment. KBP uses its α-solenoid concave face and edge loops to bind the kinesin motor domain, and selected structure-guided mutations disrupt KBP inhibition of kinesin transport in cells. The KBP-interacting motor domain surface contains motifs exclusively conserved in KBP-interacting kinesins, suggesting a basis for kinesin selectivity. | |||||||||||||||||||||
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 | 6zph.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zph.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 6zph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/6zph ftp://data.pdbj.org/pub/pdb/validation_reports/zp/6zph | HTTPS FTP |
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-Related structure data
Related structure data | 11339MC 6zpgC 6zpiC 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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1 |
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-Components
#1: Protein | Mass: 71913.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIFBP, KBP, KIAA1279, KIF1BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96EK5 |
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#2: Protein | Mass: 41986.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF15, KLP2, KNSL7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NS87 |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-MG / |
Has ligand of interest | N |
-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: Kinesin binding protein complexed with Kif15 motor domain cryo-EM density Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.072 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | 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 |
Image recording | Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Details: Movies were dose weighted. |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement |
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EM software | Name: RELION / Category: final Euler assignment |
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7513 / Symmetry type: POINT |