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- EMDB-70498: Tubulin cofactors D,E,G bound to tubulin dimer. Class 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-70498
TitleTubulin cofactors D,E,G bound to tubulin dimer. Class 2
Map data
Sample
  • Complex: Tubulin cofactors D,E,G bound to tubulin dimer
KeywordsMicrotubule / Tubulin / Tubulin cofactors / CYTOSOLIC PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsTaheri A / Al-bassam J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structures of the tubulin cofactors reveal the molecular basis of alpha/beta-tubulin biogenesis.
Authors: Aryan Taheri / Zhoaqian Wang / Bharti Singal / Fei Guo / Jawdat Al-Bassam /
Abstract: Microtubule polarity and dynamic polymerization arise from the self-association properties of the αβ-tubulin heterodimer. For decades, it has remained unclear how the tubulin cofactors TBCD, TBCE, ...Microtubule polarity and dynamic polymerization arise from the self-association properties of the αβ-tubulin heterodimer. For decades, it has remained unclear how the tubulin cofactors TBCD, TBCE, TBCC, and the Arl2 GTPase mediate the biogenesis of αβ-tubulin from individual α- and β-tubulins. Here, we use cryo-electron microscopy to determine structures of tubulin cofactors bound to αβ-tubulin. TBCD, TBCE, and Arl2 form a heterotrimeric cage-like assembly, we term TBC-DEG, around the αβ-tubulin heterodimer. The TBC-DEG-αβ-tubulin structures show that TBC-DEG wraps around β-tubulin while TBCE extends along α-tubulin. The TBC-DEG/TBCC-αβ-tubulin structures reveal that TBCC forms multi-domain interactions with Arl2 and TBCD to engage the αβ-tubulin intradimer-interface, promoting TBCE rotation while TBCD holds β-tubulin. TBCC engages the GTP-bound Arl2, multiple sites of TBCD, and the native αβ-tubulin intradimer interface near the α-tubulin N-site GTP. Together, these structures uncover transition states for αβ-tubulin biogenesis and degradation, suggesting a vise-like, GTP-hydrolysis-dependent mechanism in which TBCC binding to TBC-DEG modulates αβ-tubulin interfaces. Our studies provide structural evidence that tubulin cofactors act as enzymatic regulators that assemble the invariant αβ-tubulin architecture. By catalyzing α- and β-tubulin biogenesis and degradation, the TBC-DEG and TBCC assemblies regulate the polymerization competency of αβ-tubulin for microtubule formation.
History
DepositionMay 5, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70498.png

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Map

FileDownload / File: emd_70498.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 400 pix.
= 529.6 Å		1.32 Å/pix.
x 400 pix.
= 529.6 Å		1.32 Å/pix.
x 400 pix.
= 529.6 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.324 Å
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Contour LevelBy AUTHOR: 0.0526
Minimum - Maximum-0.004931196 - 1.7970706
Average (Standard dev.)0.0006113673 (±0.018086087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 529.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_70498_additional_1.map
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Half map: #2

Fileemd_70498_half_map_1.map
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Half map: #1

Fileemd_70498_half_map_2.map
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Sample components

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Entire : Tubulin cofactors D,E,G bound to tubulin dimer

EntireName: Tubulin cofactors D,E,G bound to tubulin dimer
Components
  • Complex: Tubulin cofactors D,E,G bound to tubulin dimer

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Supramolecule #1: Tubulin cofactors D,E,G bound to tubulin dimer

SupramoleculeName: Tubulin cofactors D,E,G bound to tubulin dimer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 132694
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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