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Yorodumi- EMDB-6187: High-resolution structures of kinesin on microtubules provide a b... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6187 | |||||||||
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Title | High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force generation | |||||||||
Map data | Microtubule decorated with monomeric human kinesin (K349 construct) having an empty nucleotide pocket. | |||||||||
Sample |
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Keywords | molecular motors / kinesin / myosin / microtubules / cytoskeletal motors | |||||||||
Function / homology | Function and homology information cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization ...cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / 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 / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / stress granule disassembly / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / mitochondrion transport along microtubule / COPI-mediated anterograde transport / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / ciliary rootlet / natural killer cell mediated cytotoxicity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / microtubule-based process / centriolar satellite / axon cytoplasm / phagocytic vesicle / MHC class II antigen presentation / dendrite cytoplasm / positive regulation of protein localization to plasma membrane / regulation of membrane potential / axon guidance / positive regulation of synaptic transmission, GABAergic / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / cellular response to type II interferon / microtubule cytoskeleton organization / microtubule cytoskeleton / Signaling by ALK fusions and activated point mutants / mitotic cell cycle / microtubule binding / vesicle / microtubule / cadherin binding / GTPase activity / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 5.0 Å | |||||||||
Authors | Shang ZG / Zhou KF / Xu C / Csencsits R / Cochran JC / Sindelar CV | |||||||||
Citation | Journal: Elife / Year: 2014 Title: High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force-generation. Authors: Zhiguo Shang / Kaifeng Zhou / Chen Xu / Roseann Csencsits / Jared C Cochran / Charles V Sindelar / Abstract: Microtubule-based transport by the kinesin motors, powered by ATP hydrolysis, is essential for a wide range of vital processes in eukaryotes. We obtained insight into this process by developing ...Microtubule-based transport by the kinesin motors, powered by ATP hydrolysis, is essential for a wide range of vital processes in eukaryotes. We obtained insight into this process by developing atomic models for no-nucleotide and ATP states of the monomeric kinesin motor domain on microtubules from cryo-EM reconstructions at 5-6 Å resolution. By comparing these models with existing X-ray structures of ADP-bound kinesin, we infer a mechanistic scheme in which microtubule attachment, mediated by a universally conserved 'linchpin' residue in kinesin (N255), triggers a clamshell opening of the nucleotide cleft and accompanying release of ADP. Binding of ATP re-closes the cleft in a manner that tightly couples to translocation of cargo, via kinesin's 'neck linker' element. These structural transitions are reminiscent of the analogous nucleotide-exchange steps in the myosin and F1-ATPase motors and inform how the two heads of a kinesin dimer 'gate' each other to promote coordinated stepping along 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_6187.map.gz | 12.7 MB | EMDB map data format | |
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Header (meta data) | emd-6187-v30.xml emd-6187.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | 400_6187.gif 80_6187.gif | 77.1 KB 4.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6187 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6187 | HTTPS FTP |
-Validation report
Summary document | emd_6187_validation.pdf.gz | 343.2 KB | Display | EMDB validaton report |
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Full document | emd_6187_full_validation.pdf.gz | 342.8 KB | Display | |
Data in XML | emd_6187_validation.xml.gz | 4.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6187 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6187 | HTTPS FTP |
-Related structure data
Related structure data | 3j8xMC 6188C 3j8yC 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_6187.map.gz / Format: CCP4 / Size: 23.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Microtubule decorated with monomeric human kinesin (K349 construct) having an empty nucleotide pocket. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.99 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 decorated with monomeric human kinesin (K349 construc...
Entire | Name: Microtubule decorated with monomeric human kinesin (K349 construct) having an empty nucleotide pocket. |
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Components |
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-Supramolecule #1000: Microtubule decorated with monomeric human kinesin (K349 construc...
Supramolecule | Name: Microtubule decorated with monomeric human kinesin (K349 construct) having an empty nucleotide pocket. type: sample / ID: 1000 Oligomeric state: One monomer of kinesin binds to one heterodimer of tubulin Number unique components: 2 |
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Molecular weight | Theoretical: 135 KDa |
-Macromolecule #1: monomeric kinesin-1A
Macromolecule | Name: monomeric kinesin-1A / type: protein_or_peptide / ID: 1 / Details: K349 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 38 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pHB40p |
-Macromolecule #2: tubulin
Macromolecule | Name: tubulin / type: protein_or_peptide / ID: 2 / Oligomeric state: heterodimer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Sus scrofa (pig) / synonym: pig |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 / Details: 25 mM PIPES, 25 mM NaCl, 2 mM MgCl2, 1 mM EGTA |
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Grid | Details: 300 mesh copper grid with homemade holey carbon |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Details | 8K x 8K Super-resolution mode was used; 10 frames total were collected. |
Date | Apr 15, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Details | Initial alignment was done using customized SPIDER scripts. Reconstruction and subsequent refinement was done by FREALIGN. |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 9.455 Å Applied symmetry - Helical parameters - Δ&Phi: 25.77 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: OTHER / Software - Name: SPIDER, FREALIGN Details: Approximately 140,000 asymmetric units were averaged in the final reconstruction. |
CTF correction | Details: done within FREALIGN |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: K / Chain - #1 - Chain ID: A / Chain - #2 - Chain ID: B |
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Software | Name: MDFF |
Details | MDFF was performed using explicit solvation, after placing active-site water coordinates identified in high-resolution crystal structures of kinesin's ATP-like state. Side chains were removed from the MDFF target potential. Following several equilibration steps, the relative strength of the EM map potential (GSCALE term) was slowly increased from 0 to 1 over the course of 10 nanoseconds. The t = 1.4 ns time point was selected to represent the final fitted model, based on the approximate convergence of the RMSD from the starting structure. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT Target criteria: RMSD from the starting structure was monitored for convergence |
Output model | PDB-3j8x: |