+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28789 | |||||||||
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Title | Apo KIF20A[1-565] class-1 in complex with a microtubule | |||||||||
Map data | Primary map, locally refined on the central asymmetric unit | |||||||||
Sample |
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Keywords | KIF20A / kinesin / motility / microtubule / tubulin / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information Mitotic Telophase/Cytokinesis / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / midbody abscission / MHC class II antigen presentation / microtubule bundle formation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport ...Mitotic Telophase/Cytokinesis / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / midbody abscission / MHC class II antigen presentation / microtubule bundle formation / 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 / 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 / microtubule motor activity / kinesin complex / intercellular bridge / microtubule-based movement / mitotic cytokinesis / regulation of cytokinesis / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein transport / mitotic cell cycle / midbody / microtubule binding / microtubule / GTPase activity / GTP binding / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Sus scrofa (pig) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Benoit MPMH / Asenjo AB / Crozet V / Ranaivoson FM / Houdusse A / Sosa H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Open Biol / Year: 2023 Title: Nucleotide-free structures of KIF20A illuminate atypical mechanochemistry in this kinesin-6. Authors: Fanomezana Moutse Ranaivoson / Vincent Crozet / Matthieu P M H Benoit / Amna Abdalla Mohammed Khalid / Carlos Kikuti / Helena Sirkia / Ahmed El Marjou / Stéphanie Miserey-Lenkei / Ana B ...Authors: Fanomezana Moutse Ranaivoson / Vincent Crozet / Matthieu P M H Benoit / Amna Abdalla Mohammed Khalid / Carlos Kikuti / Helena Sirkia / Ahmed El Marjou / Stéphanie Miserey-Lenkei / Ana B Asenjo / Hernando Sosa / Christoph F Schmidt / Steven S Rosenfeld / Anne Houdusse / Abstract: KIF20A is a critical kinesin for cell division and a promising anti-cancer drug target. The mechanisms underlying its cellular roles remain elusive. Interestingly, unusual coupling between the ...KIF20A is a critical kinesin for cell division and a promising anti-cancer drug target. The mechanisms underlying its cellular roles remain elusive. Interestingly, unusual coupling between the nucleotide- and microtubule-binding sites of this kinesin-6 has been reported, but little is known about how its divergent sequence leads to atypical motility properties. We present here the first high-resolution structure of its motor domain that delineates the highly unusual structural features of this motor, including a long L6 insertion that integrates into the core of the motor domain and that drastically affects allostery and ATPase activity. Together with the high-resolution cryo-electron microscopy microtubule-bound KIF20A structure that reveals the microtubule-binding interface, we dissect the peculiarities of the KIF20A sequence that influence its mechanochemistry, leading to low motility compared to other kinesins. Structural and functional insights from the KIF20A pre-power stroke conformation highlight the role of extended insertions in shaping the motor's mechanochemical cycle. Essential for force production and processivity is the length of the neck linker in kinesins. We highlight here the role of the sequence preceding the neck linker in controlling its backward docking and show that a neck linker four times longer than that in kinesin-1 is required for the activity of this motor. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28789.map.gz | 28.8 MB | EMDB map data format | |
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Header (meta data) | emd-28789-v30.xml emd-28789.xml | 22.9 KB 22.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28789_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_28789.png | 139.7 KB | ||
Masks | emd_28789_msk_1.map emd_28789_msk_2.map emd_28789_msk_3.map emd_28789_msk_4.map | 274.6 MB 274.6 MB 274.6 MB 274.6 MB | Mask map | |
Filedesc metadata | emd-28789.cif.gz | 8 KB | ||
Others | emd_28789_half_map_1.map.gz emd_28789_half_map_2.map.gz | 218.9 MB 218.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28789 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28789 | HTTPS FTP |
-Validation report
Summary document | emd_28789_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_28789_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_28789_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | emd_28789_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28789 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28789 | HTTPS FTP |
-Related structure data
Related structure data | 8f1aMC 8bjsC 8f18C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28789.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Primary map, locally refined on the central asymmetric unit | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.844 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28789_msk_1.map | ||||||||||||
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Density Histograms |
-Mask #2
File | emd_28789_msk_2.map | ||||||||||||
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Density Histograms |
-Mask #3
File | emd_28789_msk_3.map | ||||||||||||
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Density Histograms |
-Mask #4
File | emd_28789_msk_4.map | ||||||||||||
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Density Histograms |
-Half map: Half map from the gold Standard refinement
File | emd_28789_half_map_1.map | ||||||||||||
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Annotation | Half map from the gold Standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map from the gold Standard refinement
File | emd_28789_half_map_2.map | ||||||||||||
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Annotation | Half map from the gold Standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : KIF20A[1-565] apo in complex with a microtubule
+Supramolecule #1: KIF20A[1-565] apo in complex with a microtubule
+Supramolecule #2: KIF20A[1-565] apo
+Supramolecule #3: 15R Microtubule
+Macromolecule #1: Tubulin alpha-1B chain
+Macromolecule #2: Tubulin beta-2B chain
+Macromolecule #3: Kinesin-like protein KIF20A
+Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #5: MAGNESIUM ION
+Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #7: TAXOL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY | ||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Average electron dose: 56.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8f1a: |