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- PDB-9edt: Tubulin cofactors D,E,G bound to tubulin dimer -

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Basic information

Entry
Database: PDB / ID: 9edt
TitleTubulin cofactors D,E,G bound to tubulin dimer
Components
  • Chromosome instability protein 1
  • Designed ankyrin repeat protein -- Darpin
  • GTP-binding protein CIN4
  • Protein PAC2
  • Tubulin alpha-1A chain
  • Tubulin beta chain
KeywordsCYTOSOLIC PROTEIN / Tubulin / cofactors / Tubulin cofactors / Tubulin biogenesis / Tubulin degradation / microtubules
Function / homology
Function and homology information


post-chaperonin tubulin folding pathway / tubulin complex assembly / motile cilium / alpha-tubulin binding / beta-tubulin binding / GTPase activator activity / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / protein folding ...post-chaperonin tubulin folding pathway / tubulin complex assembly / motile cilium / alpha-tubulin binding / beta-tubulin binding / GTPase activator activity / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / protein folding / mitotic cell cycle / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Tubulin-specific chaperone D-like, ARM repeats / Tubulin-folding cofactor D / Tubulin-specific chaperone D-like, ARM repeat / ADP-ribosylation factor-like protein 2/3 / : / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain ...: / Tubulin-specific chaperone D-like, ARM repeats / Tubulin-folding cofactor D / Tubulin-specific chaperone D-like, ARM repeat / ADP-ribosylation factor-like protein 2/3 / : / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Leucine Rich repeat / 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 / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1A chain / Tubulin beta chain / GTP-binding protein CIN4 / Protein PAC2 / Chromosome instability protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Sus scrofa (pig)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTaheri, A. / Al-bassam, J.
Funding support United States, 1items
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
DepositionNov 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Chromosome instability protein 1
G: GTP-binding protein CIN4
A: Tubulin alpha-1A chain
B: Tubulin beta chain
F: Designed ankyrin repeat protein -- Darpin
E: Protein PAC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,0959
Polymers299,6066
Non-polymers1,4903
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 6 molecules DGABFE

#1: Protein Chromosome instability protein 1


Mass: 117608.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CIN1, YOR349W, O6350 / Production host: Escherichia coli (E. coli) / References: UniProt: P40987
#2: Protein GTP-binding protein CIN4 / Chromosome instability protein 4


Mass: 22096.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CIN4, GTP1, UGX1, YMR138W, YM9375.07 / Production host: Escherichia coli (E. coli) / References: UniProt: P39110
#3: Protein Tubulin alpha-1A chain / Alpha-tubulin 1 / Tubulin alpha-1 chain


Mass: 50121.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550
#4: Protein Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#5: Protein Designed ankyrin repeat protein -- Darpin


Mass: 17955.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#6: Protein Protein PAC2


Mass: 41916.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chain E contains a well-resolved C-terminal region that was modeled with full side-chain identities. Density for the LRR and CAP-Gly domains is weaker and discontinuous, consistent with ...Details: Chain E contains a well-resolved C-terminal region that was modeled with full side-chain identities. Density for the LRR and CAP-Gly domains is weaker and discontinuous, consistent with flexibility of this portion of the protein in the complex. Therefore, residues in these regions are modeled as poly-alanine to represent the backbone trace and overall topology only (listed as UNK in the entry). Side-chain identities are not asserted in these low-density regions. The sequence register is anchored by the well-resolved C-terminal domain and supported by the AlphaFold prediction.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAC2, YER007W / Production host: Escherichia coli (E. coli) / References: UniProt: P39937

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Non-polymers , 2 types, 3 molecules

#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tubulin cofactors D,E,G bound to tubulin dimer / Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21rc1_5156:model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 275487 / Symmetry type: POINT

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