+
Open data
-
Basic information
Entry | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CaKip3[2-482] - ADP-AlFx in complex with a microtubule | ||||||||||||
![]() | Primary map, locally refined on the central asymmetric unit | ||||||||||||
![]() |
| ||||||||||||
![]() | Kip3 / ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Function / homology | ![]() tubulin-dependent ATPase activity / plus-end specific microtubule depolymerization / regulation of mitotic spindle elongation / mitotic spindle astral microtubule / meiotic sister chromatid segregation / 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 / mitotic spindle astral microtubule / meiotic sister chromatid segregation / 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | helical reconstruction / ![]() | ||||||||||||
![]() | Benoit MPMH / Asenjo AB / Hunter B / Allingham J / Sosa H | ||||||||||||
Funding support | ![]() ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 31.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 24.6 KB 24.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.7 KB | Display | ![]() |
Images | ![]() | 150.3 KB | ||
Masks | ![]() ![]() ![]() ![]() | 274.6 MB 274.6 MB 274.6 MB 274.6 MB | ![]() | |
Filedesc metadata | ![]() | 8 KB | ||
Others | ![]() ![]() | 219.7 MB 219.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tqyMC ![]() 7lffC ![]() 7tqxC ![]() 7tqzC ![]() 7tr0C ![]() 7tr1C ![]() 7tr2C ![]() 7tr3C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Primary map, locally refined on the central asymmetric unit | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.849 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Mask #2
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Mask #3
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Mask #4
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map from the gold Standard refinement
File | emd_26075_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map from the gold Standard refinement | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map from the gold Standard refinement
File | emd_26075_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map from the gold Standard refinement | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
+Entire : CaKip3[2-482] - ADP-AlFx in complex with a microtubule
+Supramolecule #1: CaKip3[2-482] - ADP-AlFx in complex with a microtubule
+Supramolecule #2: CaKip3[2-482] - ADP-AlFx
+Supramolecule #3: 15R Microtubule
+Macromolecule #1: Kinesin-like protein
+Macromolecule #2: Tubulin alpha-1B chain
+Macromolecule #3: Tubulin beta-2B chain
+Macromolecule #4: ALUMINUM FLUORIDE
+Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #6: MAGNESIUM ION
+Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #8: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #9: TAXOL
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | helical reconstruction |
Aggregation state | filament |
-
Sample preparation
Buffer | pH: 6.8 Component:
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: UltrAuFoil R2/2 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Average electron dose: 63.28 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
---|---|
Output model | ![]() PDB-7tqy: |