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Yorodumi- EMDB-5916: Cryo-Electron Microscopy of Nucleotide-free Kinesin motor domain ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5916 | |||||||||
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Title | Cryo-Electron Microscopy of Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule | |||||||||
Map data | 3D structure of Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule | |||||||||
Sample |
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Keywords | KIF5C / nucleotide-free kinesin / Rigor-conformation / GMPCPP-MT / Axonal transport / transport protein | |||||||||
Function / homology | Function and homology information distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / motor neuron axon guidance / plus-end-directed microtubule motor activity / microtubule motor activity / ciliary rootlet ...distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / motor neuron axon guidance / plus-end-directed microtubule motor activity / microtubule motor activity / ciliary rootlet / kinesin complex / synaptic vesicle transport / postsynaptic cytosol / mRNA transport / axonal growth cone / axon cytoplasm / dendrite cytoplasm / axon guidance / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / neuron projection / GTPase activity / neuronal cell body / dendrite / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 8.1 Å | |||||||||
Authors | Morikawa M / Yajima H / Nitta R / Inoue S / Ogura T / Sato C / Hirokawa N | |||||||||
Citation | Journal: EMBO J / Year: 2015 Title: X-ray and Cryo-EM structures reveal mutual conformational changes of Kinesin and GTP-state microtubules upon binding. Authors: Manatsu Morikawa / Hiroaki Yajima / Ryo Nitta / Shigeyuki Inoue / Toshihiko Ogura / Chikara Sato / Nobutaka Hirokawa / Abstract: The molecular motor kinesin moves along microtubules using energy from ATP hydrolysis in an initial step coupled with ADP release. In neurons, kinesin-1/KIF5C preferentially binds to the GTP-state ...The molecular motor kinesin moves along microtubules using energy from ATP hydrolysis in an initial step coupled with ADP release. In neurons, kinesin-1/KIF5C preferentially binds to the GTP-state microtubules over GDP-state microtubules to selectively enter an axon among many processes; however, because the atomic structure of nucleotide-free KIF5C is unavailable, its molecular mechanism remains unresolved. Here, the crystal structure of nucleotide-free KIF5C and the cryo-electron microscopic structure of nucleotide-free KIF5C complexed with the GTP-state microtubule are presented. The structures illustrate mutual conformational changes induced by interaction between the GTP-state microtubule and KIF5C. KIF5C acquires the 'rigor conformation', where mobile switches I and II are stabilized through L11 and the initial portion of the neck-linker, facilitating effective ADP release and the weak-to-strong transition of KIF5C microtubule affinity. Conformational changes to tubulin strengthen the longitudinal contacts of the GTP-state microtubule in a similar manner to GDP-taxol microtubules. These results and functional analyses provide the molecular mechanism of the preferential binding of KIF5C to GTP-state microtubules. | |||||||||
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_5916.map.gz | 179.5 KB | EMDB map data format | |
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Header (meta data) | emd-5916-v30.xml emd-5916.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_5916.tif | 316.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5916 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5916 | HTTPS FTP |
-Validation report
Summary document | emd_5916_validation.pdf.gz | 308.6 KB | Display | EMDB validaton report |
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Full document | emd_5916_full_validation.pdf.gz | 308.1 KB | Display | |
Data in XML | emd_5916_validation.xml.gz | 4.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5916 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5916 | HTTPS FTP |
-Related structure data
Related structure data | 3j6hMC 3wrdC 3x2tC M: atomic model generated by this map C: citing same article (ref.) |
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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_5916.map.gz / Format: CCP4 / Size: 199.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D structure of Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.5 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 : Cryo-Electron Microscopy of Nucleotide-free Kinesin motor domain ...
Entire | Name: Cryo-Electron Microscopy of Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule |
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Components |
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-Supramolecule #1000: Cryo-Electron Microscopy of Nucleotide-free Kinesin motor domain ...
Supramolecule | Name: Cryo-Electron Microscopy of Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule type: sample / ID: 1000 Oligomeric state: One kineisn motor domain binds to one tubulin dimers Number unique components: 3 |
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-Macromolecule #1: TUBULIN ALPHA CHAIN
Macromolecule | Name: TUBULIN ALPHA CHAIN / type: protein_or_peptide / ID: 1 / Name.synonym: alpha tubulin / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Sus scrofa (pig) / Tissue: Brain |
Sequence | UniProtKB: Tubulin alpha-1A chain |
-Macromolecule #2: TUBULIN BETA CHAIN
Macromolecule | Name: TUBULIN BETA CHAIN / type: protein_or_peptide / ID: 2 / Name.synonym: beta tubulin / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Sus scrofa (pig) / Tissue: Brain |
Sequence | UniProtKB: Tubulin beta chain |
-Macromolecule #3: Kinesin heavy chain isoform 5C motor domain
Macromolecule | Name: Kinesin heavy chain isoform 5C motor domain / type: protein_or_peptide / ID: 3 / Name.synonym: KIF5C motor domain / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pET21b |
Sequence | UniProtKB: Kinesin heavy chain isoform 5C |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 / Details: 100mM PIPES, 1mM EGTA, 1mM MgCl2 |
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Staining | Type: NEGATIVE / Details: No staining |
Grid | Details: 300 mesh copper grid with thin carbon support, glow discharged in amylamine atmosphere |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 100 K / Instrument: LEICA KF80 / Method: On grid blotting (Microtubule, KIF5C) |
-Electron microscopy
Microscope | JEOL 2010F |
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Date | Aug 18, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Average electron dose: 7 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 40000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder: Liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The particles were selected along individual microtubules using an automatic processing program. |
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CTF correction | Details: Each filament |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: OTHER / Software - Name: MATLAB, ImagicV / Number images used: 302000 |
Final two d classification | Number classes: 18 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera, Modeller |
Details | Initial local fitting was done using Chimera, and for some loops Modeller was used. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT Target criteria: Cross-correlation, Average map value, Atoms inside the contour |
Output model | PDB-3j6h: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: K |
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Software | Name: Chimera, Modeller |
Details | Initial local fitting was done using Chimera, and for some loops Modeller was used. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT Target criteria: Cross-correlation, Average map value, Atoms inside the contour |
Output model | PDB-3j6h: |