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- EMDB-18664: Structure of the native microtubule lattice nucleated from the ye... -

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Basic information

Entry
Database: EMDB / ID: EMD-18664
TitleStructure of the native microtubule lattice nucleated from the yeast spindle pole body
Map data
Sample
  • Organelle or cellular component: y-Tubulin Ring Complex capping the microtubule minus end
    • Protein or peptide: Tubulin alpha-1 chain
    • Protein or peptide: Tubulin beta chain
KeywordsMicrotubule nucleation / MTOC / y-tubulin / SPB / CELL CYCLE
Function / homology
Function and homology information


nuclear migration by microtubule mediated pushing forces / nuclear division / Platelet degranulation / homologous chromosome segregation / nuclear migration along microtubule / tubulin complex / mitotic sister chromatid segregation / nuclear periphery / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...nuclear migration by microtubule mediated pushing forces / nuclear division / Platelet degranulation / homologous chromosome segregation / nuclear migration along microtubule / tubulin complex / mitotic sister chromatid segregation / nuclear periphery / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 ...Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 6.6 Å
AuthorsDendooven T / Yatskevich S / Burt A / Bellini D / Kilmartin J / Barford D
Funding support United Kingdom, Germany, 3 items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
Boehringer Ingelheim Fonds (BIF) Germany
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structure of the native γ-tubulin ring complex capping spindle microtubules.
Authors: Tom Dendooven / Stanislau Yatskevich / Alister Burt / Zhuo A Chen / Dom Bellini / Juri Rappsilber / John V Kilmartin / David Barford /
Abstract: Microtubule (MT) filaments, composed of α/β-tubulin dimers, are fundamental to cellular architecture, function and organismal development. They are nucleated from MT organizing centers by the ...Microtubule (MT) filaments, composed of α/β-tubulin dimers, are fundamental to cellular architecture, function and organismal development. They are nucleated from MT organizing centers by the evolutionarily conserved γ-tubulin ring complex (γTuRC). However, the molecular mechanism of nucleation remains elusive. Here we used cryo-electron tomography to determine the structure of the native γTuRC capping the minus end of a MT in the context of enriched budding yeast spindles. In our structure, γTuRC presents a ring of γ-tubulin subunits to seed nucleation of exclusively 13-protofilament MTs, adopting an active closed conformation to function as a perfect geometric template for MT nucleation. Our cryo-electron tomography reconstruction revealed that a coiled-coil protein staples the first row of α/β-tubulin of the MT to alternating positions along the γ-tubulin ring of γTuRC. This positioning of α/β-tubulin onto γTuRC suggests a role for the coiled-coil protein in augmenting γTuRC-mediated MT nucleation. Based on our results, we describe a molecular model for budding yeast γTuRC activation and MT nucleation.
History
DepositionOct 17, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18664.png

Downloads & links

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Map

FileDownload / File: emd_18664.map.gz / Format: CCP4 / Size: 36.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 212 pix.
= 699.6 Å		3.3 Å/pix.
x 212 pix.
= 699.6 Å		3.3 Å/pix.
x 212 pix.
= 699.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00511
Minimum - Maximum-0.013861193 - 0.023770025
Average (Standard dev.)0.0001417335 (±0.0015512103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions212212212
Spacing212212212
CellA=B=C: 699.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18664_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_18664_half_map_2.map
Projections & Slices
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Sample components

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Entire : y-Tubulin Ring Complex capping the microtubule minus end

EntireName: y-Tubulin Ring Complex capping the microtubule minus end
Components
  • Organelle or cellular component: y-Tubulin Ring Complex capping the microtubule minus end
    • Protein or peptide: Tubulin alpha-1 chain
    • Protein or peptide: Tubulin beta chain

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Supramolecule #1: y-Tubulin Ring Complex capping the microtubule minus end

SupramoleculeName: y-Tubulin Ring Complex capping the microtubule minus end
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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: 13 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 49.853867 KDa
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: 13 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 50.967457 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 6.53
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 130704
ExtractionNumber tomograms: 364 / Number images used: 31720
Final angle assignmentType: MAXIMUM LIKELIHOOD

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