+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8755 | ||||||||||||||||||||||||
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Title | Yeast tubulin polymerized with GTP in vitro | ||||||||||||||||||||||||
Map data | Yeast microtubule polymerized in vitro with GTP | ||||||||||||||||||||||||
Sample |
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Keywords | Cytoskeleton / tubulin / HYDROLASE | ||||||||||||||||||||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | ||||||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||||||||
Authors | Howes SC / Geyer EA | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: J Cell Biol / Year: 2017 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8755.map.gz | 482 MB | EMDB map data format | |
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Header (meta data) | emd-8755-v30.xml emd-8755.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_8755.png | 121.2 KB | ||
Filedesc metadata | emd-8755.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8755 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8755 | HTTPS FTP |
-Validation report
Summary document | emd_8755_validation.pdf.gz | 568.5 KB | Display | EMDB validaton report |
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Full document | emd_8755_full_validation.pdf.gz | 568.1 KB | Display | |
Data in XML | emd_8755_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | emd_8755_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8755 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8755 | HTTPS FTP |
-Related structure data
Related structure data | 5w3fMC 8756C 8757C 8758C 8759C 5w3hC 5w3jC C: citing same article (ref.) M: atomic model generated by this map |
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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_8755.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Yeast microtubule polymerized in vitro with GTP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 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 : Dynamic microtubule lattice
Entire | Name: Dynamic microtubule lattice |
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Components |
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-Supramolecule #1: Dynamic microtubule lattice
Supramolecule | Name: Dynamic microtubule lattice / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
-Macromolecule #1: Tubulin alpha-1 chain
Macromolecule | Name: Tubulin alpha-1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 49.853867 KDa |
Sequence | String: MREVISINVG QAGCQIGNAC WELYSLEHGI KPDGHLEDGL SKPKGGEEGF STFFHETGYG KFVPRAIYVD LEPNVIDEVR NGPYKDLFH PEQLISGKED AANNYARGHY TVGREILGDV LDRIRKLADQ CDGLQGFLFT HSLGGGTGSG LGSLLLEELS A EYGKKSKL ...String: MREVISINVG QAGCQIGNAC WELYSLEHGI KPDGHLEDGL SKPKGGEEGF STFFHETGYG KFVPRAIYVD LEPNVIDEVR NGPYKDLFH PEQLISGKED AANNYARGHY TVGREILGDV LDRIRKLADQ CDGLQGFLFT HSLGGGTGSG LGSLLLEELS A EYGKKSKL EFAVYPAPQV STSVVEPYNT VLTTHTTLEH ADCTFMVDNE AIYDMCKRNL DIPRPSFANL NNLIAQVVSS VT ASLRFDG SLNVDLNEFQ TNLVPYPRIH FPLVSYSPVL SKSKAFHESN SVSEITNACF EPGNQMVKCD PRDGKYMATC LLY RGDVVT RDVQRAVEQV KNKKTVQLVD WCPTGFKIGI CYEPPTATPN SQLATVDRAV CMLSNTTSIA EAWKRIDRKF DLMY AKRAF VHWYVGEGME EGEFTEARED LAALERDYIE VGADSYAEEE EF UniProtKB: Tubulin alpha-1 chain |
-Macromolecule #2: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 50.967457 KDa |
Sequence | String: MREIIHISTG QCGNQIGAAF WETICGEHGL DFNGTYHGHD DIQKERLNVY FNEASSGKWV PRSINVDLEP GTIDAVRNSA IGNLFRPDN YIFGQSSAGN VWAKGHYTEG AELVDSVMDV IRREAEGCDS LQGFQITHSL GGGTGSGMGT LLISKIREEF P DRMMATFS ...String: MREIIHISTG QCGNQIGAAF WETICGEHGL DFNGTYHGHD DIQKERLNVY FNEASSGKWV PRSINVDLEP GTIDAVRNSA IGNLFRPDN YIFGQSSAGN VWAKGHYTEG AELVDSVMDV IRREAEGCDS LQGFQITHSL GGGTGSGMGT LLISKIREEF P DRMMATFS VLPSPKTSDT VVEPYNATLS VHQLVEHSDE TFCIDNEALY DICQRTLKLN QPSYGDLNNL VSSVMSGVTT SL RYPGQLN SDLRKLAVNL VPFPRLHFFM VGYAPLTAIG SQSFRSLTVP ELTQQMFDAK NMMAAADPRN GRYLTVAAFF RGK VSVKEV EDEMHKVQSK NSDYFVEWIP NNVQTAVCSV APQGLDMAAT FIANSTSIQE LFKRVGDQFS AMFKRKAFLH WYTS EGMDE LEFSEAESNM NDLVSEYQQY QEATVEDDEE VDENGDFGAP QNQDEPITEN FE UniProtKB: Tubulin beta chain |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 6.9 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 303 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 10.4 Å Applied symmetry - Helical parameters - Δ&Phi: -29.85 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 42871 |
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Startup model | Type of model: EMDB MAP |
Final angle assignment | Type: NOT APPLICABLE |