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Yorodumi- EMDB-1036: Structure of a fast kinesin: implications for ATPase mechanism an... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1036 | |||||||||
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Title | Structure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules. | |||||||||
Map data | Neurospora crassa kinesin monomer (nK355) AMP-PNP state | |||||||||
Sample |
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Biological species | Neurospora crassa (fungus) | |||||||||
Method | helical reconstruction / cryo EM / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Krebs A | |||||||||
Citation | Journal: EMBO J / Year: 2001 Title: Structure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules. Authors: Y H Song / A Marx / J Müller / G Woehlke / M Schliwa / A Krebs / A Hoenger / E Mandelkow / Abstract: We determined the crystal structure of the motor domain of the fast fungal kinesin from Neurospora crassa (NcKin). The structure has several unique features. (i) Loop 11 in the switch 2 region is ...We determined the crystal structure of the motor domain of the fast fungal kinesin from Neurospora crassa (NcKin). The structure has several unique features. (i) Loop 11 in the switch 2 region is ordered and enables one to describe the complete nucleotide-binding pocket, including three inter-switch salt bridges between switch 1 and 2. (ii) Loop 9 in the switch 1 region bends outwards, making the nucleotide-binding pocket very wide. The displacement in switch 1 resembles that of the G-protein ras complexed with its guanosine nucleotide exchange factor. (iii) Loop 5 in the entrance to the nucleotide-binding pocket is remarkably long and interacts with the ribose of ATP. (iv) The linker and neck region is not well defined, indicating that it is mobile. (v) Image reconstructions of ice-embedded microtubules decorated with NcKin show that it interacts with several tubulin subunits, including a central beta-tubulin monomer and the two flanking alpha-tubulin monomers within the microtubule protofilament. Comparison of NcKin with other kinesins, myosin and G-proteins suggests that the rate-limiting step of ADP release is accelerated in the fungal kinesin and accounts for the unusually high velocity and ATPase activity. | |||||||||
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_1036.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-1036-v30.xml emd-1036.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | 1036.gif | 64.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1036 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1036 | HTTPS FTP |
-Validation report
Summary document | emd_1036_validation.pdf.gz | 250.5 KB | Display | EMDB validaton report |
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Full document | emd_1036_full_validation.pdf.gz | 249.6 KB | Display | |
Data in XML | emd_1036_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1036 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1036 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1036.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Neurospora crassa kinesin monomer (nK355) AMP-PNP state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.526 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 : neurospora crassa kinesin monomer
Entire | Name: neurospora crassa kinesin monomer |
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Components |
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-Supramolecule #1000: neurospora crassa kinesin monomer
Supramolecule | Name: neurospora crassa kinesin monomer / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 2 |
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-Macromolecule #1: neurospora crassakinesin
Macromolecule | Name: neurospora crassakinesin / type: protein_or_peptide / ID: 1 / Name.synonym: molecular motor / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes / Database: NCBI |
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Source (natural) | Organism: Neurospora crassa (fungus) / synonym: neurospora |
-Macromolecule #2: tubulin
Macromolecule | Name: tubulin / type: protein_or_peptide / ID: 2 / Name.synonym: microtubules / Number of copies: 1 / Oligomeric state: hetero dimer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Neurospora crassa (fungus) / synonym: neurospora / Tissue: brain / Cell: neuronal cells / Location in cell: cytoplasm |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 6.9 Details: Pipes 20mM, 50 mM NaCl, 5mM mgcl,1mM Mg-ATP, 20um taxol. |
Staining | Type: NEGATIVE / Details: ice-embedded |
Grid | Details: holey grids |
Vitrification | Cryogen name: PROPANE / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: self made |
-Electron microscopy
Microscope | FEI/PHILIPS CM120T |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 21 µm / Number real images: 18 / Average electron dose: 5 e/Å2 / Bits/pixel: 16 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 100 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 37000 |
Sample stage | Specimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Phoelix, Suprim Details: Final maps from 36 averaged datasets = 18 helical tubes |
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