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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6779 | |||||||||||||||
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Title | GDP-microtubule complexed with nucleotide-free KIF5C | |||||||||||||||
![]() | KIF5C(nucleotide-free) and Microtubule(GDP) | |||||||||||||||
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Function / homology | ![]() Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 5.35 Å | |||||||||||||||
![]() | Morikawa M / Shigematsu H / Nitta R / Hirokawa N | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport. Authors: Tomohiro Shima / Manatsu Morikawa / Junichi Kaneshiro / Taketoshi Kambara / Shinji Kamimura / Toshiki Yagi / Hiroyuki Iwamoto / Sotaro Uemura / Hideki Shigematsu / Mikako Shirouzu / Taro ...Authors: Tomohiro Shima / Manatsu Morikawa / Junichi Kaneshiro / Taketoshi Kambara / Shinji Kamimura / Toshiki Yagi / Hiroyuki Iwamoto / Sotaro Uemura / Hideki Shigematsu / Mikako Shirouzu / Taro Ichimura / Tomonobu M Watanabe / Ryo Nitta / Yasushi Okada / Nobutaka Hirokawa / ![]() ![]() Abstract: Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the ...Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the guidance cue for polarized transport in neurons, but the underlying mechanisms are still poorly understood. Here, we report that kinesin-1 binding changes the microtubule lattice and promotes further kinesin-1 binding. This high-affinity state requires the binding of kinesin-1 in the nucleotide-free state. Microtubules return to the initial low-affinity state by washing out the binding kinesin-1 or by the binding of non-hydrolyzable ATP analogue AMPPNP to kinesin-1. X-ray fiber diffraction, fluorescence speckle microscopy, and second-harmonic generation microscopy, as well as cryo-EM, collectively demonstrated that the binding of nucleotide-free kinesin-1 to GDP microtubules changes the conformation of the GDP microtubule to a conformation resembling the GTP microtubule. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.4 KB 15.4 KB | Display Display | ![]() |
Images | ![]() | 313 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xxtMC ![]() 6781C ![]() 6782C ![]() 6783C ![]() 5xxvC ![]() 5xxwC ![]() 5xxxC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | KIF5C(nucleotide-free) and Microtubule(GDP) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.284 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : GDP-microtubule complexed with nucleotide-free KIF5C
Entire | Name: GDP-microtubule complexed with nucleotide-free KIF5C |
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Components |
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-Supramolecule #1: GDP-microtubule complexed with nucleotide-free KIF5C
Supramolecule | Name: GDP-microtubule complexed with nucleotide-free KIF5C / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() Recombinant plasmid: pET21b |
-Macromolecule #1: Tubulin alpha-1A chain
Macromolecule | Name: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 48.638793 KDa |
Sequence | String: RECISIHVGQ AGVQIGNACW ELYCLEHGIQ PDGQMPSDKT IGGGDDSFNT FFSETGAGKH VPRAVFVDLE PTVIDEVRTG TYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFSVFHS FGGGTGSGFT SLLMERLSVD Y GKKSKLEF ...String: RECISIHVGQ AGVQIGNACW ELYCLEHGIQ PDGQMPSDKT IGGGDDSFNT FFSETGAGKH VPRAVFVDLE PTVIDEVRTG TYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFSVFHS FGGGTGSGFT SLLMERLSVD Y GKKSKLEF SIYPAPQVST AVVEPYNSIL TTHTTLEHSD CAFMVDNEAI YDICRRNLDI ERPTYTNLNR LIGQIVSSIT AS LRFDGAL NVDLTEFQTN LVPYPRGHFP LATYAPVISA EKAYHEQLSV AEITNACFEP ANQMVKCDPR HGKYMACCLL YRG DVVPKD VNAAIATIKT KRTIQFVDWC PTGFKVGINY EPPTVVPGGD LAKVQRAVCM LSNTTAIAEA WARLDHKFDL MYAK RAFVH WYVGEGMEEG EFSEAREDMA ALEKDYEEVG VDS |
-Macromolecule #2: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 47.809746 KDa |
Sequence | String: REIVHIQAGQ CGNQIGAKFW EVISDEHGID PTGSYHGDSD LQLERINVYY NEAAGNKYVP RAILVDLEPG TMDSVRSGPF GQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP D RIMNTFSV ...String: REIVHIQAGQ CGNQIGAKFW EVISDEHGID PTGSYHGDSD LQLERINVYY NEAAGNKYVP RAILVDLEPG TMDSVRSGPF GQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP D RIMNTFSV VPSPKVSDTV VEPYNATLSV HQLVENTDET YCIDNEALYD ICFRTLKLTT PTYGDLNHLV SATMSGVTTC LR FPGQLNA DLRKLAVNMV PFPRLHFFMP GFAPLTSRGS QQYRALTVPE LTQQMFDAKN MMAACDPRHG RYLTVAAVFR GRM SMKEVD EQMLNVQNKN SSYFVEWIPN NVKTAVCDIP PRGLKMSATF IGNSTAIQEL FKRISEQFTA MFRRKAFLHW YTGE GMDEM EFTEAESNMN DLVSEYQQYQ D |
-Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 9 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 9 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 9 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ![]() ChemComp-GDP: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 36 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 8.70662 Å Applied symmetry - Helical parameters - Δ&Phi: -25.7617 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 5.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9) / Number images used: 17173 |
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Startup model | Type of model: EMDB MAP EMDB ID: |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-5xxt: |