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- EMDB-63572: Cryo-EM structure of the TBC-D-Arl2-beta-tubulin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63572
TitleCryo-EM structure of the TBC-D-Arl2-beta-tubulin complex
Map data
Sample
  • Complex: Complex of tubulin specific chaperone D, Arl2 and beta-tubulin
    • Complex: TBCD-Arl2
      • Protein or peptide: Tubulin-specific chaperone D
      • Protein or peptide: ADP-ribosylation factor-like protein 2
    • Complex: beta-tubulin
      • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordschaperone / complex
Function / homology
Function and homology information


Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / post-chaperonin tubulin folding pathway / 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 ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / post-chaperonin tubulin folding pathway / 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 / 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 / adherens junction assembly / centrosome cycle / positive regulation of cell-substrate adhesion / Recruitment of NuMA to mitotic centrosomes / regulation of glycolytic process / 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 / negative regulation of cell-substrate adhesion / bicellular tight junction / beta-tubulin binding / intercellular bridge / spindle assembly / positive regulation of microtubule polymerization / GTPase activator activity / 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 / microtubule / ciliary basal body / mitochondrial matrix / GTPase activity / ubiquitin protein ligase binding / centrosome / GTP binding / nucleolus / mitochondrion / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tubulin-specific chaperone D, C-terminal / Tubulin-folding cofactor D / Tubulin folding cofactor D C terminal / Tubulin-specific chaperone D-like, ARM repeat / ADP-ribosylation factor-like protein 2 / ADP-ribosylation factor-like protein 2/3 / 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 ...Tubulin-specific chaperone D, C-terminal / Tubulin-folding cofactor D / Tubulin folding cofactor D C terminal / Tubulin-specific chaperone D-like, ARM repeat / ADP-ribosylation factor-like protein 2 / ADP-ribosylation factor-like protein 2/3 / 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 / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADP-ribosylation factor-like protein 2 / Tubulin beta chain / Tubulin-specific chaperone D
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsSeong YJ / Kim HM / Byun KM / Park YW / Roh SH
Funding support Korea, Republic Of, 1 items
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 YJ / Kim HM / Byun KM / Park YW / Roh SH
History
DepositionFeb 26, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63572.png

Downloads & links

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Map

FileDownload / File: emd_63572.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 380 pix.
= 273.79 Å		0.72 Å/pix.
x 380 pix.
= 273.79 Å		0.72 Å/pix.
x 380 pix.
= 273.79 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7205 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.10903449 - 2.3745246
Average (Standard dev.)0.0012466937 (±0.024899662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 273.79 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63572_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_63572_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63572_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of tubulin specific chaperone D, Arl2 and beta-tubulin

EntireName: Complex of tubulin specific chaperone D, Arl2 and beta-tubulin
Components
  • Complex: Complex of tubulin specific chaperone D, Arl2 and beta-tubulin
    • Complex: TBCD-Arl2
      • Protein or peptide: Tubulin-specific chaperone D
      • Protein or peptide: ADP-ribosylation factor-like protein 2
    • Complex: beta-tubulin
      • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of tubulin specific chaperone D, Arl2 and beta-tubulin

SupramoleculeName: Complex of tubulin specific chaperone D, Arl2 and beta-tubulin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 200 KDa

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Supramolecule #2: TBCD-Arl2

SupramoleculeName: TBCD-Arl2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: beta-tubulin

SupramoleculeName: beta-tubulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Sus scrofa (pig)

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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: 132.752516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MALSDEPAAG GPEEEAEDET LAFGAALEAF GESAETRALL GRLREVHGGG AEREVALERF RVIMDKYQEQ PHLLDPHLEW MMNLLLDIV QDQTSPASLV HLAFKFLYII TKVRGYKTFL RLFPHEVADV EPVLDLVTIQ NPKDHEAWET RYMLLLWLSV T CLIPFDFS ...String:
MALSDEPAAG GPEEEAEDET LAFGAALEAF GESAETRALL GRLREVHGGG AEREVALERF RVIMDKYQEQ PHLLDPHLEW MMNLLLDIV QDQTSPASLV HLAFKFLYII TKVRGYKTFL RLFPHEVADV EPVLDLVTIQ NPKDHEAWET RYMLLLWLSV T CLIPFDFS RLDGNLLTQP GQARMSIMDR ILQIAESYLI VSDKARDAAA VLVSRFITRP DVKQSKMAEF LDWSLCNLAR SS FQTMQGV ITMDGTLQAL AQIFKHGKRE DCLPYAATVL RCLDGCRLPE SNQTLLRKLG VKLVQRLGLT FLKPKVAAWR YQR GCRSLA ANLQLLTQGQ SEQKPLILTE DDDEDDDVPE GVERVIEQLL VGLKDKDTVV RWSAAKGIGR MAGRLPRALA DDVV GSVLD CFSFQETDKA WHGGCLALAE LGRRGLLLPS RLVDVVAVIL KALTYDEKRG ACSVGTNVRD AACYVCWAFA RAYEP QELK PFVTAISSAL VIAAVFDRDI NCRRAASAAF QENVGRQGTF PHGIDILTTA DYFAVGNRSN CFLVISVFIA GFPEYT QPM IDHLVTMKIS HWDGVIRELA ARALHNLAQQ APEFSATQVF PRLLSMTLSP DLHMRHGSIL ACAEVAYALY KLAAQEN RP VTDHLDEQAV QGLKQIHQQL YDRQLYRGLG GQLMRQAVCV LIEKLSLSKM PFRGDTVIDG WQWLINDTLR HLHLISSH S RQQMKDAAVS ALAALCSEYY MKEPGEADPA IQEELITQYL AELRNPEEMT RCGFSLALGA LPGFLLKGRL QQVLTGLRA VTHTSPEDVS FAESRRDGLK AIARICQTVG VKAGAPDEAV CGENVSQIYC ALLGCMDDYT TDSRGDVGTW VRKAAMTSLM DLTLLLARS QPELIEAHTC ERIMCCVAQQ ASEKIDRFRA HAASVFLTLL HFDSPPIPHV PHRGELEKLF PRSDVASVNW S APSQAFPR ITQLLGLPTY RYHVLLGLVV SLGGLTESTI RHSTQSLFEY MKGIQSDPQA LGSFSGTLLQ IFEDNLLNER VS VPLLKTL DHVLTHGCFD IFTTEEDHPF AVKLLALCKK EIKNSKDIQK LLSGIAVFCE MVQFPGDVRR QALLQLCLLL CHR FPLIRK TTASQVYETL LTYSDVVGAD VLDEVVTVLS DTAWDAELAV VREQRNRLCD LLGVPRPQLV PQPGAC

UniProtKB: Tubulin-specific chaperone D

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

MacromoleculeName: ADP-ribosylation factor-like protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.903992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 #3: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.717629 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQVFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMAVT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEED FGEEAEEEA

UniProtKB: Tubulin beta chain

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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 BIOQUANTUM (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: 2.0 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: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123124
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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