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Open data
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Basic information
Entry | Database: PDB / ID: 5w3f | ||||||||||||||||||||||||
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Title | Yeast tubulin polymerized with GTP in vitro | ||||||||||||||||||||||||
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![]() | HYDROLASE / Cytoskeleton / tubulin | ||||||||||||||||||||||||
Function / homology | ![]() nuclear migration by microtubule mediated pushing forces / nuclear division / mitotic spindle elongation / nuclear migration along microtubule / homologous chromosome segregation / Platelet degranulation / positive regulation of intracellular protein transport / tubulin complex / mitotic sister chromatid segregation / microtubule-based process ...nuclear migration by microtubule mediated pushing forces / nuclear division / mitotic spindle elongation / nuclear migration along microtubule / homologous chromosome segregation / Platelet degranulation / positive regulation of intracellular protein transport / tubulin complex / mitotic sister chromatid segregation / microtubule-based process / mitotic spindle assembly / cytoplasmic microtubule organization / cytoskeleton organization / nuclear periphery / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / mitotic cell cycle / microtubule / hydrolase activity / response to antibiotic / GTPase activity / GTP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||||||||
![]() | Howes, S.C. / Geyer, E.A. / LaFrance, B. / Zhang, R. / Kellogg, E.H. / Westermann, S. / Rice, L.M. / Nogales, E. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural differences between yeast and mammalian microtubules revealed by cryo-EM. Authors: Stuart C Howes / Elisabeth A Geyer / Benjamin LaFrance / Rui Zhang / Elizabeth H Kellogg / Stefan Westermann / Luke M Rice / Eva Nogales / ![]() ![]() Abstract: Microtubules are polymers of αβ-tubulin heterodimers essential for all eukaryotes. Despite sequence conservation, there are significant structural differences between microtubules assembled in ...Microtubules are polymers of αβ-tubulin heterodimers essential for all eukaryotes. Despite sequence conservation, there are significant structural differences between microtubules assembled in vitro from mammalian or budding yeast tubulin. Yeast MTs were not observed to undergo compaction at the interdimer interface as seen for mammalian microtubules upon GTP hydrolysis. Lack of compaction might reflect slower GTP hydrolysis or a different degree of allosteric coupling in the lattice. The microtubule plus end-tracking protein Bim1 binds yeast microtubules both between αβ-tubulin heterodimers, as seen for other organisms, and within tubulin dimers, but binds mammalian tubulin only at interdimer contacts. At the concentrations used in cryo-electron microscopy, Bim1 causes the compaction of yeast microtubules and induces their rapid disassembly. Our studies demonstrate structural differences between yeast and mammalian microtubules that likely underlie their differing polymerization dynamics. These differences may reflect adaptations to the demands of different cell size or range of physiological growth temperatures. | ||||||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.8 KB | Display | ![]() |
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PDB format | ![]() | 265.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8755MC ![]() 8756C ![]() 8757C ![]() 8758C ![]() 8759C ![]() 5w3hC ![]() 5w3jC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 49853.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P09733 |
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#2: Protein | Mass: 50967.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P02557 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GTP / |
#5: Chemical | ChemComp-GDP / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Dynamic microtubule lattice / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 6.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 303 K |
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Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 28 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 20 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Helical symmerty | Angular rotation/subunit: -29.85 ° / Axial rise/subunit: 10.4 Å / Axial symmetry: C1 | ||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42871 / Symmetry type: HELICAL |