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- PDB-9m1m: Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex ... -

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Basic information

Entry
Database: PDB / ID: 9m1m
TitleCryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
Components
  • (Tubulin-specific chaperone ...) x 3
  • ADP-ribosylation factor-like protein 2
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCHAPERONE / complex
Function / homology
Function and homology information


peripheral nervous system neuron axonogenesis / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / post-chaperonin tubulin folding pathway / muscle atrophy / cell morphogenesis involved in neuron differentiation / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 ...peripheral nervous system neuron axonogenesis / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / post-chaperonin tubulin folding pathway / muscle atrophy / cell morphogenesis involved in neuron differentiation / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of mitotic centrosome proteins and complexes / odontoblast differentiation / photoreceptor connecting cilium / Post-chaperonin tubulin folding pathway / negative regulation of GTPase activity / tubulin complex assembly / bicellular tight junction assembly / Neutrophil degranulation / maintenance of protein location in nucleus / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / adherens junction assembly / centrosome cycle / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / positive regulation of cell-substrate adhesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / regulation of glycolytic process / COPI-mediated anterograde transport / regulation of aerobic respiration / negative regulation of microtubule polymerization / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / regulation of microtubule polymerization / lateral plasma membrane / developmental growth / negative regulation of cell-substrate adhesion / bicellular tight junction / alpha-tubulin binding / beta-tubulin binding / intercellular bridge / spindle assembly / positive regulation of microtubule polymerization / tubulin binding / GTPase activator activity / adult locomotory behavior / mitotic spindle organization / post-embryonic development / adherens junction / structural constituent of cytoskeleton / mitochondrial intermembrane space / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / RAS processing / mitotic spindle / GDP binding / protein folding / mitotic cell cycle / protein-folding chaperone binding / microtubule cytoskeleton / cell body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton / ciliary basal body / mitochondrial matrix / GTPase activity / ubiquitin protein ligase binding / centrosome / GTP binding / nucleolus / endoplasmic reticulum / mitochondrion / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tubulin-specific chaperone C, N-terminal / TBCC, N-terminal domain superfamily / Tubulin-specific chaperone C N-terminal domain / Tubulin-specific chaperone C / Tubulin binding cofactor C-like domain / Tubulin binding cofactor C / Tubulin-specific chaperone D, C-terminal / Tubulin-folding cofactor D / TBCE, ubiquitin-like (Ubl) domain / Tubulin folding cofactor D C terminal ...Tubulin-specific chaperone C, N-terminal / TBCC, N-terminal domain superfamily / Tubulin-specific chaperone C N-terminal domain / Tubulin-specific chaperone C / Tubulin binding cofactor C-like domain / Tubulin binding cofactor C / Tubulin-specific chaperone D, C-terminal / Tubulin-folding cofactor D / TBCE, ubiquitin-like (Ubl) domain / Tubulin folding cofactor D C terminal / Tubulin-specific chaperone D-like, ARM repeat / ADP-ribosylation factor-like protein 2 / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Ubiquitin-like domain / ADP-ribosylation factor-like protein 2/3 / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / 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 / 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 / Rab subfamily of small GTPases / Leucine-rich repeat domain superfamily / Armadillo-like helical / Small GTP-binding protein domain / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / ADP-ribosylation factor-like protein 2 / Tubulin-specific chaperone E / Tubulin-specific chaperone C / Tubulin alpha-1B chain / Tubulin beta chain / Tubulin-specific chaperone D
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.21 Å
AuthorsSeong, Y.J. / Kim, H.M. / Byun, K.M. / Park, Y.W. / Roh, S.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Science / Year: 2025
Title: Structural dissection of alpha beta-tubulin heterodimer assembly and disassembly by human tubulin-specific chaperones
Authors: Seong, Y.J. / Kim, H.M. / Byun, K.M. / Park, Y.W. / Roh, S.H.
History
DepositionFeb 26, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Tubulin-specific chaperone C
D: Tubulin-specific chaperone D
E: Tubulin-specific chaperone E
G: ADP-ribosylation factor-like protein 2
a: Tubulin alpha-1B chain
b: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,94713
Polymers352,3016
Non-polymers1,6467
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Tubulin-specific chaperone ... , 3 types, 3 molecules CDE

#1: Protein Tubulin-specific chaperone C / Tubulin-folding cofactor C / CFC


Mass: 39300.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBCC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q15814
#2: Protein Tubulin-specific chaperone D / Beta-tubulin cofactor D / tfcD / SSD-1 / Tubulin-folding cofactor D


Mass: 132752.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBCD, KIAA0988, SSD1, TFCD, PP1096 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9BTW9
#3: Protein Tubulin-specific chaperone E / Tubulin-folding cofactor E


Mass: 59422.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBCE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q15813

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Protein , 3 types, 3 molecules Gab

#4: Protein ADP-ribosylation factor-like protein 2


Mass: 20903.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P36404
#5: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBA1B / Production host: Sus scrofa (pig)
References: UniProt: Q2XVP4, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#6: Protein Tubulin beta chain / Tubulin beta-5 chain


Mass: 49717.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBB, TUBB5 / Production host: Sus scrofa (pig) / References: UniProt: Q767L7

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Non-polymers , 4 types, 7 molecules

#7: 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
#8: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: 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

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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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of tubulin specific chaperone D, E, C, Arl2, alpha-tubulin and beta-tubulin with GDP-AlFxCOMPLEX#1-#60RECOMBINANT
2TBC-DEC-Arl2COMPLEX#1-#41RECOMBINANT
3alpha-beta-tubulinCOMPLEX#5-#61RECOMBINANT
Molecular weightValue: 0.35 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Sus scrofa (pig)9823
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Sus scrofa (pig)9823
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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 729421 / Symmetry type: POINT

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