[English] 日本語
Yorodumi- EMDB-11340: Microtubule complexed with Kif15 motor domain. Symmetrised asymme... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11340 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Microtubule complexed with Kif15 motor domain. Symmetrised asymmetric unit | |||||||||||||||||||||
Map data | Kif15 motor domain (AMPPNP bound) complexed with microtubule (asymmetric unit). | |||||||||||||||||||||
Sample |
| |||||||||||||||||||||
Function / homology | Function and homology information plus-end kinesin complex / centrosome separation / 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 ...plus-end kinesin complex / centrosome separation / 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 / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / microtubule-based movement / cytoskeletal motor activity / mitotic spindle assembly / MHC class II antigen presentation / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle pole / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / microtubule binding / microtubule / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Pig (pig) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||||||||
Authors | Atherton J / Hummel JJA / Olieric N / Locke J / Pena A / Rosenfeld SS / Steinmetz MO / Hoogenraad CC / Moores CA | |||||||||||||||||||||
Funding support | United Kingdom, Switzerland, United States, 6 items
| |||||||||||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11340.map.gz | 511.6 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11340-v30.xml emd-11340.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
Images | emd_11340.png | 137.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11340 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11340 | HTTPS FTP |
-Validation report
Summary document | emd_11340_validation.pdf.gz | 202.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_11340_full_validation.pdf.gz | 202.1 KB | Display | |
Data in XML | emd_11340_validation.xml.gz | 4.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11340 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11340 | HTTPS FTP |
-Related structure data
Related structure data | 6zpiMC 6zpgC 6zphC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_11340.map.gz / Format: CCP4 / Size: 2.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Kif15 motor domain (AMPPNP bound) complexed with microtubule (asymmetric unit). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Kif15 motor domain (AMPPNP bound) complexed with microtubule. Sym...
+Supramolecule #1: Kif15 motor domain (AMPPNP bound) complexed with microtubule. Sym...
+Supramolecule #2: Kif15 motor domain
+Supramolecule #3: Microtubule
+Macromolecule #1: Kinesin-like protein KIF15
+Macromolecule #2: Tubulin alpha-1B chain
+Macromolecule #3: Tubulin beta chain
+Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+Macromolecule #5: MAGNESIUM ION
+Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #7: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #8: TAXOL
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 / Details: Movies were dose weighted. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL / Details: Kinesin-1 decorated microtubule (synthetic model). |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Software - details: MiRP protocol / Number images used: 12674 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |