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Yorodumi- EMDB-1788: Doublecortin-stabilised microtubules at secondary structure resolution -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1788 | |||||||||
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Title | Doublecortin-stabilised microtubules at secondary structure resolution | |||||||||
Map data | This is the corner between 4 tubulin dimers bound by doublecortin, in 13-protofilament microtubules | |||||||||
Sample |
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Keywords | Tubulin / MAP / microtubule / stabilisation / doublecortin | |||||||||
Function / homology | Function and homology information axoneme assembly / Neurofascin interactions / positive regulation of axon guidance / microtubule associated complex / microtubule organizing center / microtubule-based process / central nervous system development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / neuron migration / structural constituent of cytoskeleton ...axoneme assembly / Neurofascin interactions / positive regulation of axon guidance / microtubule associated complex / microtubule organizing center / microtubule-based process / central nervous system development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / neuron migration / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / retina development in camera-type eye / nervous system development / mitotic cell cycle / microtubule binding / microtubule / cytoskeleton / hydrolase activity / intracellular signal transduction / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / protein kinase binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) / Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / negative staining / Resolution: 8.2 Å | |||||||||
Authors | Fourniol FJ / Sindelar CV / Amigues B / Clare D / Thomas G / Perderiset M / Francis F / Houdusse A / Moores CA | |||||||||
Citation | Journal: J Cell Biol / Year: 2010 Title: Template-free 13-protofilament microtubule-MAP assembly visualized at 8 A resolution. Authors: Franck J Fourniol / Charles V Sindelar / Béatrice Amigues / Daniel K Clare / Geraint Thomas / Mylène Perderiset / Fiona Francis / Anne Houdusse / Carolyn A Moores / Abstract: Microtubule-associated proteins (MAPs) are essential for regulating and organizing cellular microtubules (MTs). However, our mechanistic understanding of MAP function is limited by a lack of detailed ...Microtubule-associated proteins (MAPs) are essential for regulating and organizing cellular microtubules (MTs). However, our mechanistic understanding of MAP function is limited by a lack of detailed structural information. Using cryo-electron microscopy and single particle algorithms, we solved the 8 Å structure of doublecortin (DCX)-stabilized MTs. Because of DCX's unusual ability to specifically nucleate and stabilize 13-protofilament MTs, our reconstruction provides unprecedented insight into the structure of MTs with an in vivo architecture, and in the absence of a stabilizing drug. DCX specifically recognizes the corner of four tubulin dimers, a binding mode ideally suited to stabilizing both lateral and longitudinal lattice contacts. A striking consequence of this is that DCX does not bind the MT seam. DCX binding on the MT surface indirectly stabilizes conserved tubulin-tubulin lateral contacts in the MT lumen, operating independently of the nucleotide bound to tubulin. DCX's exquisite binding selectivity uncovers important insights into regulation of cellular MTs. | |||||||||
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_1788.map.gz | 104 KB | EMDB map data format | |
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Header (meta data) | emd-1788-v30.xml emd-1788.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | EMD-1788.png | 315.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1788 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1788 | HTTPS FTP |
-Related structure data
Related structure data | 2xrpMC 1787C 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_1788.map.gz / Format: CCP4 / Size: 319.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the corner between 4 tubulin dimers bound by doublecortin, in 13-protofilament microtubules | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 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 : Microtubules co-polymerised with doublecortin
Entire | Name: Microtubules co-polymerised with doublecortin |
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Components |
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-Supramolecule #1000: Microtubules co-polymerised with doublecortin
Supramolecule | Name: Microtubules co-polymerised with doublecortin / type: sample / ID: 1000 / Oligomeric state: 13-protofilament microtubule / Number unique components: 2 |
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-Macromolecule #1: Tubulin alpha-1D chain
Macromolecule | Name: Tubulin alpha-1D chain / type: protein_or_peptide / ID: 1 / Name.synonym: Alpha Tubulin / Oligomeric state: Heterodimer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Bovine / Tissue: Brain / Location in cell: Cytoplasm |
Sequence | InterPro: Alpha tubulin |
-Macromolecule #2: Tubulin beta-2B chain
Macromolecule | Name: Tubulin beta-2B chain / type: protein_or_peptide / ID: 2 / Name.synonym: Beta Tubulin / Oligomeric state: Heterodimer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Bovine / Tissue: Brain / Location in cell: Cytoplasm |
Sequence | InterPro: Beta tubulin, autoregulation binding site |
-Macromolecule #3: Doublecortin
Macromolecule | Name: Doublecortin / type: protein_or_peptide / ID: 3 / Name.synonym: DCX / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Cytoplasm |
Recombinant expression | Organism: Spodoptera frugiperda (Sf9) / Recombinant plasmid: pFastBac |
Sequence | InterPro: Doublecortin domain |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 Details: 80mM Pipes, 1mM EGTA, 3mM MgCl2, 1mM TCEP, 0.5mM GTP |
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Staining | Type: NEGATIVE / Details: cryo-EM |
Grid | Details: 300 mesh lacey carbon grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot (FEI) / Method: Chamber at 37 degrees C, blot 2s |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.76 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
Temperature | Average: 93 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 63 / Average electron dose: 15 e/Å2 / Details: Images were binned with a factor of 2 / Bits/pixel: 8 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: done with FREALIGN |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, FREALIGN Details: Approximately 168,000 asymmetric units were averaged together in the final map |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: UCSF Chimera, Flex-EM |
Details | Protocol: Rigid body. 4 tubulin monomers were fitted separately in 3D map, which was zoned around the subunits, and multiple subunit fitting was refined in Flex-EM |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation |
Output model | PDB-2xrp: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: UCSF Chimera, Flex-EM |
Details | PDBEntryID_givenInChain. Protocol: Rigid body. 4 tubulin monomers were fitted separately in 3D map, which was zoned around the subunits, and multiple subunit fitting was refined in Flex-EM |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation |
Output model | PDB-2xrp: |