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- EMDB-74459: Tubulin cofactors D and E bound to beta tubulin -

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Basic information

Entry
Database: EMDB / ID: EMD-74459
TitleTubulin cofactors D and E bound to beta tubulin
Map data
Sample
  • Complex: Complex of human tubulin folding cofactors D,E bound to beta tubulin
    • Protein or peptide: Tubulin-specific chaperone D
    • Protein or peptide: Tubulin-specific chaperone E
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsTubulin / cofactor / chaperone / microtubule / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


cell morphogenesis involved in neuron differentiation / post-chaperonin tubulin folding pathway / Post-chaperonin tubulin folding pathway / tubulin complex assembly / bicellular tight junction assembly / adherens junction assembly / negative regulation of microtubule polymerization / negative regulation of cell-substrate adhesion / bicellular tight junction / lateral 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 / adherens junction assembly / negative regulation of microtubule polymerization / negative regulation of cell-substrate adhesion / bicellular tight junction / lateral plasma membrane / alpha-tubulin binding / beta-tubulin binding / microtubule-based process / GTPase activator activity / mitotic spindle organization / adherens junction / microtubule cytoskeleton organization / structural constituent of cytoskeleton / mitotic cell cycle / microtubule / protein folding / protein-folding chaperone binding / centrosome / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Tubulin-specific chaperone D, C-terminal / TBCE, ubiquitin-like (Ubl) domain / 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 / CAP-Gly domain signature. ...Tubulin-specific chaperone D, C-terminal / TBCE, ubiquitin-like (Ubl) domain / 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 / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / 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 / Armadillo-like helical / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tubulin beta chain / 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: 4.78 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 28, 2026-
Current statusOct 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74459.png

Downloads & links

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Map

FileDownload / File: emd_74459.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 520 pix.
= 457.6 Å		0.88 Å/pix.
x 520 pix.
= 457.6 Å		0.88 Å/pix.
x 520 pix.
= 457.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0621
Minimum - Maximum-0.0017655187 - 3.1251674
Average (Standard dev.)0.00047069538 (±0.016856272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 457.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_74459_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74459_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of human tubulin folding cofactors D,E bound to beta tubulin

EntireName: Complex of human tubulin folding cofactors D,E bound to beta tubulin
Components
  • Complex: Complex of human tubulin folding cofactors D,E bound to beta tubulin
    • Protein or peptide: Tubulin-specific chaperone D
    • Protein or peptide: Tubulin-specific chaperone E
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of human tubulin folding cofactors D,E bound to beta tubulin

SupramoleculeName: Complex of human tubulin folding cofactors D,E bound to beta tubulin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Tubulin-specific chaperone D

MacromoleculeName: Tubulin-specific chaperone D / type: protein_or_peptide / ID: 1 / 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 #2: Tubulin-specific chaperone E

MacromoleculeName: Tubulin-specific chaperone E / type: protein_or_peptide / ID: 2 / 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 #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: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / 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 GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 231300
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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