9EEB | pdb_00009eeb

Tubulin cofactors D,E,G bound to tubulin dimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structures of the tubulin cofactors reveal the molecular basis of alpha/beta-tubulin biogenesis.

Taheri, A.Wang, Z.Singal, B.Guo, F.Al-Bassam, J.

(2025) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-68142-0
  • Primary Citation of Related Structures:  
    9EDR, 9EDS, 9EDT, 9EEB

  • PubMed 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, 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.


  • Organizational Affiliation
    • Molecular Cellular Biology Department, University of California, Davis, CA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PAC2A [auth E]347Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PAC2YER007W
UniProt
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Go to UniProtKB:  P39937
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UniProt GroupP39937
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein CIN4B [auth G]191Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CIN4GTP1UGX1YMR138WYM9375.07
UniProt
Find proteins for P39110 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP39110
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chainC [auth B]445Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
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UniProt GroupP02554
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DESIGNED ANKYRIN REPEAT PROTEIN -- DARPinD [auth F]169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome instability protein 1E [auth D]1,020Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CIN1YOR349WO6350
UniProt
Find proteins for P40987 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1A chainF [auth A]451Sus scrofaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P02550 (Sus scrofa)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5156:
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-04
    Type: Initial release