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- EMDB-8759: Yeast microtubule assembled using the slowly hydrolyzable analogu... -

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Basic information

Entry
Database: EMDB / ID: EMD-8759
TitleYeast microtubule assembled using the slowly hydrolyzable analogue GTPgammaS
Map dataYeast microtubule assembled using the slowly hydrolyzable analogue GTPgammaS
Sample
  • Complex: Yeast microtubule assembled using the slowly hydrolyzable analogue GTPgammaS
    • Protein or peptide: Tubulin alpha-1
    • Protein or peptide: Tubulin beta
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)
Methodhelical reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsHowes SC / Geyer EA / LaFrance B / Zhang R / Kellogg EH / Westermann S / Rice LM / Nogales E
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) releaseJun 28, 2017-
Map releaseJul 12, 2017-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8759.png

Downloads & links

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Map

FileDownload / File: emd_8759.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast microtubule assembled using the slowly hydrolyzable analogue GTPgammaS
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-5.0270987 - 16.394259999999999
Average (Standard dev.)0.062632605 (±1.0369987)
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
start NX/NY/NZ000
NX/NY/NZ416416416
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-5.02716.3940.063

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Supplemental data

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Sample components

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Entire : Yeast microtubule assembled using the slowly hydrolyzable analogu...

EntireName: Yeast microtubule assembled using the slowly hydrolyzable analogue GTPgammaS
Components
  • Complex: Yeast microtubule assembled using the slowly hydrolyzable analogue GTPgammaS
    • Protein or peptide: Tubulin alpha-1
    • Protein or peptide: Tubulin beta

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Supramolecule #1: Yeast microtubule assembled using the slowly hydrolyzable analogu...

SupramoleculeName: Yeast microtubule assembled using the slowly hydrolyzable analogue GTPgammaS
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

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Macromolecule #1: Tubulin alpha-1

MacromoleculeName: Tubulin alpha-1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MREVISINVG QAGCQIGNAC WELYSLEHGI KPDGHLEDGL SKPKGGEEGF STFFHETGYG KFVPRAIYV DLEPNVIDEV RNGPYKDLFH PEQLISGKED AANNYARGHY TVGREILGDV L DRIRKLAD QCDGLQGFLF THSLGGGTGS GLGSLLLEEL SAEYGKKSKL ...String:
MREVISINVG QAGCQIGNAC WELYSLEHGI KPDGHLEDGL SKPKGGEEGF STFFHETGYG KFVPRAIYV DLEPNVIDEV RNGPYKDLFH PEQLISGKED AANNYARGHY TVGREILGDV L DRIRKLAD QCDGLQGFLF THSLGGGTGS GLGSLLLEEL SAEYGKKSKL EFAVYPAPQV ST SVVEPYN TVLTTHTTLE HADCTFMVDN EAIYDMCKRN LDIPRPSFAN LNNLIAQVVS SVT ASLRFD GSLNVDLNEF QTNLVPYPRI HFPLVSYSPV LSKSKAFHES NSVSEITNAC FEPG NQMVK CDPRDGKYMA TCLLYRGDVV TRDVQRAVEQ VKNKKTVQLV DWCPTGFKIG ICYEP PTAT PNSQLATVDR AVCMLSNTTS IAEAWKRIDR KFDLMYAKRA FVHWYVGEGM EEGEFT EAR EDLAALERDY IEVGADSYAE EEEF

UniProtKB: Tubulin alpha-1 chain

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Macromolecule #2: Tubulin beta

MacromoleculeName: Tubulin beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MREIIHISTG QCGNQIGAAF WETICGEHGL DFNGTYHGHD DIQKERLNVY FNEASSGKWV PRSINVDLE PGTIDAVRNS AIGNLFRPDN YIFGQSSAGN VWAKGHYTEG AELVDSVMDV I RREAEGCD SLQGFQITHS LGGGTGSGMG TLLISKIREE FPDRMMATFS ...String:
MREIIHISTG QCGNQIGAAF WETICGEHGL DFNGTYHGHD DIQKERLNVY FNEASSGKWV PRSINVDLE PGTIDAVRNS AIGNLFRPDN YIFGQSSAGN VWAKGHYTEG AELVDSVMDV I RREAEGCD SLQGFQITHS LGGGTGSGMG TLLISKIREE FPDRMMATFS VLPSPKTSDT VV EPYNATL SVHQLVEHSD ETFCIDNEAL YDICQRTLKL NQPSYGDLNN LVSSVMSGVT TSL RYPGQL NSDLRKLAVN LVPFPRLHFF MVGYAPLTAI GSQSFRSLTV PELTQQMFDA KNMM AAADP RNGRYLTVAA FFRGKVSVKE VEDEMHKVQS KNSDYFVEWI PNNVQTAVCS VAPQG LDMA ATFIANSTSI QELFKRVGDQ FSAMFKRKAF LHWYTSEGMD ELEFSEAESN MNDLVS EYQ QYQEATVEDD EEVDENGDFG APQNQDEPIT ENFE

UniProtKB: Tubulin beta chain

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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
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: 10.3 Å
Applied symmetry - Helical parameters - Δ&Phi: -29.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 4999

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