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- EMDB-74458: Tubulin cofactors D,E,G bound to beta tubulin -

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Basic information

Entry
Database: EMDB / ID: EMD-74458
TitleTubulin cofactors D,E,G bound to beta tubulin
Map data
Sample
  • Complex: Complex of TBC cofactors purified with endogenous beta tubulin
    • Protein or peptide: Tubulin-specific chaperone E
    • Protein or peptide: Tubulin-specific chaperone D
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: ADP-ribosylation factor-like protein 2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsTubulin / tubulin cofactors / TBC / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / cell morphogenesis involved in neuron differentiation / post-chaperonin tubulin folding pathway / Post-chaperonin tubulin folding pathway / tubulin complex assembly / bicellular tight junction assembly / negative regulation of GTPase activity / positive regulation of cell-substrate adhesion / maintenance of protein location in nucleus / adherens junction assembly ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / cell morphogenesis involved in neuron differentiation / post-chaperonin tubulin folding pathway / Post-chaperonin tubulin folding pathway / tubulin complex assembly / bicellular tight junction assembly / negative regulation of GTPase activity / positive regulation of cell-substrate adhesion / maintenance of protein location in nucleus / adherens junction assembly / centrosome cycle / regulation of glycolytic process / regulation of aerobic respiration / negative regulation of microtubule polymerization / regulation of microtubule polymerization / negative regulation of cell-substrate adhesion / bicellular tight junction / lateral plasma membrane / alpha-tubulin binding / positive regulation of microtubule polymerization / beta-tubulin binding / microtubule-based process / GTPase activator activity / mitotic spindle organization / adherens junction / microtubule cytoskeleton organization / mitochondrial intermembrane space / structural constituent of cytoskeleton / microtubule cytoskeleton / RAS processing / GDP binding / mitotic cell cycle / microtubule / protein folding / protein-folding chaperone binding / mitochondrial matrix / centrosome / GTPase activity / nucleolus / GTP binding / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Tubulin-specific chaperone D, C-terminal / TBCE, ubiquitin-like (Ubl) domain / ADP-ribosylation factor-like protein 2 / Tubulin folding cofactor D C terminal / Tubulin-folding cofactor D / : / : / Tubulin-specific chaperone D-like, ARM repeat / Tubulin-specific chaperone D-like, ARM repeats / Ubiquitin-like domain ...Tubulin-specific chaperone D, C-terminal / TBCE, ubiquitin-like (Ubl) domain / ADP-ribosylation factor-like protein 2 / Tubulin folding cofactor D C terminal / Tubulin-folding cofactor D / : / : / Tubulin-specific chaperone D-like, ARM repeat / Tubulin-specific chaperone D-like, ARM repeats / Ubiquitin-like domain / 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 / 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 domain superfamily / Rab subfamily of small GTPases / 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
Tubulin beta chain / ADP-ribosylation factor-like protein 2 / Tubulin-specific chaperone E / Tubulin-specific chaperone D
Similarity search - Component
Biological speciesHomo sapiens (human) / Trichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 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: Sci Adv / Year: 2026
Title: A unified mechanism for tubulin cofactors catalyzing α/β-tubulin biogenesis and degradation.
Authors: Aryan Taheri / Md Ashaduzzaman / Vishv Gill / Julian A Eskin / Jawdat Al-Bassam /
Abstract: Microtubules polymerize from cytoplasmic pools of soluble αβ-tubulin heterodimers that support diverse cellular functions. The tubulin cofactors, TBCC, TBCD, and TBCE and the Arl2 GTPase, form TBC- ...Microtubules polymerize from cytoplasmic pools of soluble αβ-tubulin heterodimers that support diverse cellular functions. The tubulin cofactors, TBCC, TBCD, and TBCE and the Arl2 GTPase, form TBC-DEG assemblies that regulate the assembly of α- and β-tubulin into heterodimers and their disassembly, yet their underlying mechanisms remain incompletely understood. Here, we reconstitute the human TBC-DE and TBC-DEG assemblies from eukaryotic cells copurified with monomeric β-tubulin intermediates and determine their cryo-EM structures. The structures reveal that TBC-DEG disassembles αβ-tubulin by releasing α-tubulin through a lever arm-like rotation in TBCE coupled to major conformational change in Arl2 upon its nucleotide release, while TBCD tightly holds β-tubulin. TBCD dissociates α-tubulin by refolding the β-tubulin H10-S8 loop at its intradimer interface. The TBC-DEG-β-tubulin or TBC-DE-β-tubulin assemblies undergo extensive back-to-back dimerization mediated by β-β-tubulin homodimers, formed through their dissociated H8 helices at unoccupied intradimer interfaces. Structural comparisons demonstrate that TBCE's mechanical rotation, driven by the Arl2 GTPase cycle, either delivers α-tubulin or removes it from beneath the TBCD-bound β-tubulin and is directionally regulated by TBCC stabilizing αβ-tubulin interfaces. Our findings suggest that TBC-DEG/TBCC catalyzing heterodimerization of α-tubulin with β-tubulin may have evolved to counteract β-tubulin's intrinsic tendency to form off-pathway toxic homodimers through its exposed α-tubulin-binding intradimer interface.
History
DepositionDec 14, 2025-
Header (metadata) releaseOct 21, 2026-
Map releaseOct 21, 2026-
UpdateOct 21, 2026-
Current statusOct 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74458.png

Downloads & links

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Map

FileDownload / File: emd_74458.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 338.56 Å		1.06 Å/pix.
x 320 pix.
= 338.56 Å		1.06 Å/pix.
x 320 pix.
= 338.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0309
Minimum - Maximum-0.0000060579223 - 1.9972537
Average (Standard dev.)0.0014116738 (±0.027461935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 338.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of TBC cofactors purified with endogenous beta tubulin

EntireName: Complex of TBC cofactors purified with endogenous beta tubulin
Components
  • Complex: Complex of TBC cofactors purified with endogenous beta tubulin
    • Protein or peptide: Tubulin-specific chaperone E
    • Protein or peptide: Tubulin-specific chaperone D
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: ADP-ribosylation factor-like protein 2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of TBC cofactors purified with endogenous beta tubulin

SupramoleculeName: Complex of TBC cofactors purified with endogenous beta tubulin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Tubulin-specific chaperone E

MacromoleculeName: Tubulin-specific chaperone E / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.42202 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSDTLTADVI GRRVEVNGEH ATVRFAGVVP PVAGPWLGVE WDNPERGKHD GSHEGTVYFK CRHPTGGSFI RPNKVNFGTD FLTAIKNRY VLEDGPEEDR KEQIVTIGNK PVETIGFDSI MKQQSQLSKL QEVSLRNCAV SCAGEKGGVA EACPNIRKVD L SKNLLSSW ...String:
MSDTLTADVI GRRVEVNGEH ATVRFAGVVP PVAGPWLGVE WDNPERGKHD GSHEGTVYFK CRHPTGGSFI RPNKVNFGTD FLTAIKNRY VLEDGPEEDR KEQIVTIGNK PVETIGFDSI MKQQSQLSKL QEVSLRNCAV SCAGEKGGVA EACPNIRKVD L SKNLLSSW DEVIHIADQL RHLEVLNVSE NKLKFPSGSV LTGTLSVLKV LVLNQTGITW AEVLRCVAGC PGLEELYLES NN IFISERP TDVLQTVKLL DLSSNQLIDE NQLYLIAHLP RLEQLILSDT GISSLHFPDA GIGCKTSMFP SLKYLVVNDN QIS QWSFFN ELEKLPSLRA LSCLRNPLTK EDKEAETARL LIIASIGQLK TLNKCEILPE ERRRAELDYR KAFGNEWKQA GGHK DPEKN RLSEEFLTAH PRYQFLCLKY GAPEDWELKT QQPLMLKNQL LTLKIKYPHQ LDQKVLEKQL PGSMTIQKVK GLLSR LLKV PVSDLLLSYE SPKKPGREIE LENDLKSLQF YSVENGDCLL VRW

UniProtKB: Tubulin-specific chaperone E

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Macromolecule #2: Tubulin-specific chaperone D

MacromoleculeName: Tubulin-specific chaperone D / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 134.214109 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MWSHPQFEKG SGSMALSDEP AAGGPEEEAE DETLAFGAAL EAFGESAETR ALLGRLREVH GGGAEREVAL ERFRVIMDKY QEQPHLLDP HLEWMMNLLL DIVQDQTSPA SLVHLAFKFL YIITKVRGYK TFLRLFPHEV ADVEPVLDLV TIQNPKDHEA W ETRYMLLL ...String:
MWSHPQFEKG SGSMALSDEP AAGGPEEEAE DETLAFGAAL EAFGESAETR ALLGRLREVH GGGAEREVAL ERFRVIMDKY QEQPHLLDP HLEWMMNLLL DIVQDQTSPA SLVHLAFKFL YIITKVRGYK TFLRLFPHEV ADVEPVLDLV TIQNPKDHEA W ETRYMLLL WLSVTCLIPF DFSRLDGNLL TQPGQARMSI MDRILQIAES YLIVSDKARD AAAVLVSRFI TRPDVKQSKM AE FLDWSLC NLARSSFQTM QGVITMDGTL QALAQIFKHG KREDCLPYAA TVLRCLDGCR LPESNQTLLR KLGVKLVQRL GLT FLKPKV AAWRYQRGCR SLAANLQLLT QGQSEQKPLI LTEDDDEDDD VPEGVERVIE QLLVGLKDKD TVVRWSAAKG IGRM AGRLP RALADDVVGS VLDCFSFQET DKAWHGGCLA LAELGRRGLL LPSRLVDVVA VILKALTYDE KRGACSVGTN VRDAA CYVC WAFARAYEPQ ELKPFVTAIS SALVIAAVFD RDINCRRAAS AAFQENVGRQ GTFPHGIDIL TTADYFAVGN RSNCFL VIS VFIAGFPEYT QPMIDHLVTM KISHWDGVIR ELAARALHNL AQQAPEFSAT QVFPRLLSMT LSPDLHMRHG SILACAE VA YALYKLAAQE NRPVTDHLDE QAVQGLKQIH QQLYDRQLYR GLGGQLMRQA VCVLIEKLSL SKMPFRGDTV IDGWQWLI N DTLRHLHLIS SHSRQQMKDA AVSALAALCS EYYMKEPGEA DPAIQEELIT QYLAELRNPE EMTRCGFSLA LGALPGFLL KGRLQQVLTG LRAVTHTSPE DVSFAESRRD GLKAIARICQ TVGVKAGAPD EAVCGENVSQ IYCALLGCMD DYTTDSRGDV GTWVRKAAM TSLMDLTLLL ARSQPELIEA HTCERIMCCV AQQASEKIDR FRAHAASVFL TLLHFDSPPI PHVPHRGELE K LFPRSDVA SVNWSAPSQA FPRITQLLGL PTYRYHVLLG LVVSLGGLTE STIRHSTQSL FEYMKGIQSD PQALGSFSGT LL QIFEDNL LNERVSVPLL KTLDHVLTHG CFDIFTTEED HPFAVKLLAL CKKEIKNSKD IQKLLSGIAV FCEMVQFPGD VRR QALLQL CLLLCHRFPL IRKTTASQVY ETLLTYSDVV GADVLDEVVT VLSDTAWDAE LAVVREQRNR LCDLLGVPRP QLVP QPGAC

UniProtKB: Tubulin-specific chaperone D

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Macromolecule #3: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 49.973805 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAEGCDC LQGFQLTHSL GGGTGAGLGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAEGCDC LQGFQLTHSL GGGTGAGLGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE SYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFI PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMMNIQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEGE FDEEEEGGDE GD

UniProtKB: Tubulin beta chain

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

MacromoleculeName: ADP-ribosylation factor-like protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.903992 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MGLLTILKKM KQKERELRLL MLGLDNAGKT TILKKFNGED IDTISPTLGF NIKTLEHRGF KLNIWDVGGQ KSLRSYWRNY FESTDGLIW VVDSADRQRM QDCQRELQSL LVEERLAGAT LLIFANKQDL PGALSSNAIR EVLELDSIRS HHWCIQGCSA V TGENLLPG IDWLLDDISS RIFTAD

UniProtKB: ADP-ribosylation factor-like protein 2

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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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 K3 (6k 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: 2.3000000000000003 µm / Nominal defocus min: 0.8 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: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 154103
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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