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- EMDB-8757: Yeast microtubule stabilized with Taxol assembled from mutated tubulin -

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Basic information

Entry
Database: EMDB / ID: EMD-8757
TitleYeast microtubule stabilized with Taxol assembled from mutated tubulin
Map dataYeast microtubule stabilized with Taxol assembled from mutated tubulin
Sample
  • Complex: Yeast microtubule stabilized with taxol assembled from mutated tubulin
    • Protein or peptide: Tubulin alpha-1 chain
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel
KeywordsCytoskeleton / tubulin / HYDROLASE
Function / homology
Function and homology information


nuclear migration by microtubule mediated pushing forces / Cilium Assembly / nuclear division / Sealing of the nuclear envelope (NE) by ESCRT-III / mitotic spindle elongation / nuclear migration along microtubule / homologous chromosome segregation / Platelet degranulation / positive regulation of intracellular protein transport / tubulin complex ...nuclear migration by microtubule mediated pushing forces / Cilium Assembly / nuclear division / Sealing of the nuclear envelope (NE) by ESCRT-III / mitotic spindle elongation / nuclear migration along microtubule / homologous chromosome segregation / Platelet degranulation / positive regulation of intracellular protein transport / tubulin complex / mitotic sister chromatid segregation / mitotic spindle assembly / microtubule-based process / cytoplasmic microtubule organization / cytoskeleton organization / Neutrophil degranulation / nuclear periphery / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / response to antibiotic / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin beta chain / Tubulin alpha-1 chain
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsHowes SC / Geyer EA
Funding support United States, 7 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1106400 United States
National Science Foundation (NSF, United States)MCB 1054947 United States
National Science Foundation (NSF, United States)1615938 United States
National Science Foundation (NSF, United States)2014177758 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM098543 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008297 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM051487 United States
CitationJournal: 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
DepositionJun 7, 2017-
Header (metadata) releaseJul 12, 2017-
Map releaseJul 19, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5w3j
  • Surface level: 5.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5w3j
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8757.png

Downloads & links

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Map

FileDownload / File: emd_8757.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast microtubule stabilized with Taxol assembled from mutated tubulin
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 5.1 / Movie #1: 5.1
Minimum - Maximum-5.4459743 - 17.861618
Average (Standard dev.)0.06592046 (±1.0013956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 675.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z675.840675.840675.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-5.44617.8620.066

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Supplemental data

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Sample components

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Entire : Yeast microtubule stabilized with taxol assembled from mutated tubulin

EntireName: Yeast microtubule stabilized with taxol assembled from mutated tubulin
Components
  • Complex: Yeast microtubule stabilized with taxol assembled from mutated tubulin
    • Protein or peptide: Tubulin alpha-1 chain
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel

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Supramolecule #1: Yeast microtubule stabilized with taxol assembled from mutated tubulin

SupramoleculeName: Yeast microtubule stabilized with taxol assembled from mutated tubulin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

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Macromolecule #1: Tubulin alpha-1 chain

MacromoleculeName: Tubulin alpha-1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 49.853867 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
SequenceString: 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

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Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 51.089668 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
SequenceString: MREIIHISTG QCGNQIGAKF WEVICDEHGL DFNGTYHGHD DIQKERLNVY FNEASSGKWV PRSINVDLEP GTIDAVRNSA IGNLFRPDN YIFGQSSAGN VWAKGHYTEG AELVDSVMDV IRREAEGCDS LQGFQITHSL GGGTGSGMGT LLISKIREEF P DRMMATFS ...String:
MREIIHISTG QCGNQIGAKF WEVICDEHGL DFNGTYHGHD DIQKERLNVY FNEASSGKWV PRSINVDLEP GTIDAVRNSA IGNLFRPDN YIFGQSSAGN VWAKGHYTEG AELVDSVMDV IRREAEGCDS LQGFQITHSL GGGTGSGMGT LLISKIREEF P DRMMATFS VLPSPKTSDT VVEPYNATLS VHQLVEHSDE TFCIDNEALY DICQRTLKLN QPSYGDLNHL VSSVMSGVTT SL RYPGQLN SDLRKLAVNL VPFPRLHFFM VGFAPLTAIG 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

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Macromolecule #6: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 6 / Number of copies: 1 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM / Paclitaxel

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6.9
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 303 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 28.0 e/Å2

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Image processing

Startup modelType of model: EMDB MAP
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 10.41 Å
Applied symmetry - Helical parameters - Δ&Phi: -29.87 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 30101

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