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Yorodumi- EMDB-21315: Cryo-EM structure of microtubule-bound KLP61F motor with tail dom... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21315 | |||||||||
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Title | Cryo-EM structure of microtubule-bound KLP61F motor with tail domain in the nucleotide-free state | |||||||||
Map data | microtubule-bound KLP61F motor with tail domain in the nucleotide-free state | |||||||||
Sample |
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Keywords | Kinesin-5 / KLP61F / microtubules / mitotic spindles / nucleotide-free state / cell cycle / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / mitotic spindle microtubule / spindle elongation / microtubule bundle formation ...aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / mitotic spindle microtubule / spindle elongation / microtubule bundle formation / positive regulation of Golgi to plasma membrane protein transport / plus-end-directed microtubule motor activity / mitotic centrosome separation / microtubule associated complex / kinesin complex / microtubule-based movement / mitotic spindle pole / Golgi organization / cytoskeletal motor activity / protein secretion / mitotic spindle assembly / mitotic spindle organization / spindle microtubule / mitotic spindle / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / cell division / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Drosophila melanogaster (fruit fly) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Bodrug T / Wilson-Kubalek EM | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Elife / Year: 2020 Title: The kinesin-5 tail domain directly modulates the mechanochemical cycle of the motor domain for anti-parallel microtubule sliding. Authors: Tatyana Bodrug / Elizabeth M Wilson-Kubalek / Stanley Nithianantham / Alex F Thompson / April Alfieri / Ignas Gaska / Jennifer Major / Garrett Debs / Sayaka Inagaki / Pedro Gutierrez / ...Authors: Tatyana Bodrug / Elizabeth M Wilson-Kubalek / Stanley Nithianantham / Alex F Thompson / April Alfieri / Ignas Gaska / Jennifer Major / Garrett Debs / Sayaka Inagaki / Pedro Gutierrez / Larisa Gheber / Richard J McKenney / Charles Vaughn Sindelar / Ronald Milligan / Jason Stumpff / Steven S Rosenfeld / Scott T Forth / Jawdat Al-Bassam / Abstract: Kinesin-5 motors organize mitotic spindles by sliding apart microtubules. They are homotetramers with dimeric motor and tail domains at both ends of a bipolar minifilament. Here, we describe a ...Kinesin-5 motors organize mitotic spindles by sliding apart microtubules. They are homotetramers with dimeric motor and tail domains at both ends of a bipolar minifilament. Here, we describe a regulatory mechanism involving direct binding between tail and motor domains and its fundamental role in microtubule sliding. Kinesin-5 tails decrease microtubule-stimulated ATP-hydrolysis by specifically engaging motor domains in the nucleotide-free or ADP states. Cryo-EM reveals that tail binding stabilizes an open motor domain ATP-active site. Full-length motors undergo slow motility and cluster together along microtubules, while tail-deleted motors exhibit rapid motility without clustering. The tail is critical for motors to zipper together two microtubules by generating substantial sliding forces. The tail is essential for mitotic spindle localization, which becomes severely reduced in tail-deleted motors. Our studies suggest a revised microtubule-sliding model, in which kinesin-5 tails stabilize motor domains in the microtubule-bound state by slowing ATP-binding, resulting in high-force production at both homotetramer ends. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21315.map.gz | 14.3 MB | EMDB map data format | |
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Header (meta data) | emd-21315-v30.xml emd-21315.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
Images | emd_21315.png | 47.8 KB | ||
Filedesc metadata | emd-21315.cif.gz | 6.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21315 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21315 | HTTPS FTP |
-Validation report
Summary document | emd_21315_validation.pdf.gz | 505.4 KB | Display | EMDB validaton report |
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Full document | emd_21315_full_validation.pdf.gz | 505 KB | Display | |
Data in XML | emd_21315_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | emd_21315_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21315 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21315 | HTTPS FTP |
-Related structure data
Related structure data | 6vppMC 6vpoC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21315.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | microtubule-bound KLP61F motor with tail domain in the nucleotide-free state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Microtubule-bound KLP61F motor with tail domain in the nucleotide...
Entire | Name: Microtubule-bound KLP61F motor with tail domain in the nucleotide-free state |
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Components |
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-Supramolecule #1: Microtubule-bound KLP61F motor with tail domain in the nucleotide...
Supramolecule | Name: Microtubule-bound KLP61F motor with tail domain in the nucleotide-free state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: microtubule
Supramolecule | Name: microtubule / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Sus scrofa (pig) |
-Supramolecule #3: KLP61F motor
Supramolecule | Name: KLP61F motor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
-Macromolecule #1: Tubulin alpha-1A chain
Macromolecule | Name: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) |
Molecular weight | Theoretical: 50.121266 KDa |
Sequence | String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRAHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YEPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY UniProtKB: Tubulin alpha-1A chain |
-Macromolecule #2: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) |
Molecular weight | Theoretical: 49.90777 KDa |
Sequence | String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA UniProtKB: Tubulin beta chain |
-Macromolecule #3: Kinesin-like protein Klp61F
Macromolecule | Name: Kinesin-like protein Klp61F / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 42.627336 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDISGGNTSR QPQKKSNQNI QVYVRVRPLN SRERCIRSAE VVDVVGPREV VTRHTLDSKL TKKFTFDRSF GPESKQCDVY SVVVSPLIE EVLNGYNCTV FAYGQTGTGK THTMVGNETA ELKSSWEDDS DIGIIPRALS HLFDELRMME VEYTMRISYL E LYNEELCD ...String: MDISGGNTSR QPQKKSNQNI QVYVRVRPLN SRERCIRSAE VVDVVGPREV VTRHTLDSKL TKKFTFDRSF GPESKQCDVY SVVVSPLIE EVLNGYNCTV FAYGQTGTGK THTMVGNETA ELKSSWEDDS DIGIIPRALS HLFDELRMME VEYTMRISYL E LYNEELCD LLSTDDTTKI RIFDDSTKKG SVIIQGLEEI PVHSKDDVYK LLEKGKERRK TATTLMNAQS SRSHTVFSIV VH IRENGIE GEDMLKIGKL NLVDLAGSEN VSKAGNEKGI RVRETVNINQ SLLTLGRVIT ALVDRAPHVP YRESKLTRLL QES LGGRTK TSIIATISPG HKDIEETLST LEYAHRAKNI QNKPEVNQKL TKKLEHHHHH H UniProtKB: Kinesin-like protein Klp61F |
-Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 6.8 |
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 17.4 Å Applied symmetry - Helical parameters - Δ&Phi: -34.61 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14570 |
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Startup model | Type of model: OTHER |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 208 / Target criteria: Correlation coefficient |
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Output model | PDB-6vpp: |