+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+88 | ||||||||||||
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Title | Cryo-EM structure of C. elegans GDP-microtubule | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Cytoskeletal protein | ||||||||||||
Function / homology | Function and homology information COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / meiotic spindle organization / embryo development ending in birth or egg hatching / centrosome localization / tubulin complex ...COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / meiotic spindle organization / embryo development ending in birth or egg hatching / centrosome localization / tubulin complex / establishment of mitotic spindle orientation / regulation of cytokinesis / spindle microtubule / protein localization / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||||||||
Authors | Chaaban, S. / Jariwala, S. / Chieh-Ting, H. / Redemann, S. / Kollman, J. / Muller-Reichert, T. / Sept, D. / Bui, K.H. / Brouhard, G.J. | ||||||||||||
Funding support | Canada, 3items
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Citation | Journal: Dev Cell / Year: 2018 Title: The Structure and Dynamics of C. elegans Tubulin Reveals the Mechanistic Basis of Microtubule Growth. Authors: Sami Chaaban / Shashank Jariwala / Chieh-Ting Hsu / Stefanie Redemann / Justin M Kollman / Thomas Müller-Reichert / David Sept / Khanh Huy Bui / Gary J Brouhard / Abstract: The dynamic instability of microtubules is a conserved and fundamental mechanism in eukaryotes. Yet microtubules from different species diverge in their growth rates, lattice structures, and ...The dynamic instability of microtubules is a conserved and fundamental mechanism in eukaryotes. Yet microtubules from different species diverge in their growth rates, lattice structures, and responses to GTP hydrolysis. Therefore, we do not know what limits microtubule growth, what determines microtubule structure, or whether the mechanisms of dynamic instability are universal. Here, we studied microtubules from the nematode C. elegans, which have strikingly fast growth rates and non-canonical lattices in vivo. Using a reconstitution approach, we discovered that C. elegans microtubules combine intrinsically fast growth with very frequent catastrophes. We solved the structure of C. elegans microtubules to 4.8 Å and discovered sequence divergence in the lateral contact loops, one of which is ordered in C. elegans but unresolved in other species. We provide direct evidence that C. elegans tubulin has a higher free energy in solution and propose a model wherein the ordering of lateral contact loops activates tubulin for growth. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6e88.cif.gz | 876.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e88.ent.gz | 733.5 KB | Display | PDB format |
PDBx/mmJSON format | 6e88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/6e88 ftp://data.pdbj.org/pub/pdb/validation_reports/e8/6e88 | HTTPS FTP |
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-Related structure data
Related structure data | 9004MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 48467.609 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / Strain: N2 / References: UniProt: P34690 #2: Protein | Mass: 47843.988 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / Strain: N2 / References: UniProt: P52275 #3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-GDP / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: microtubule / Type: ORGANELLE OR CELLULAR COMPONENT Details: C. elegans microtubules polymerized in the presence of GTP Entity ID: #1-#2 / Source: NATURAL |
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Molecular weight | Value: 165 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Caenorhabditis elegans (invertebrata) / Strain: N2 |
Buffer solution | pH: 6.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 29.33 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16574 / Symmetry type: POINT |
Atomic model building | Protocol: FLEXIBLE FIT |