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- EMDB-51972: Full gamma-tubulin ring complex composed of the Candida albicans ... -

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Basic information

Entry
Database: EMDB / ID: EMD-51972
TitleFull gamma-tubulin ring complex composed of the Candida albicans gamma-tubulin small complex in complex with Spc72 CM1
Map dataConsensus map for cryo-EM reconstruction of a full, 14-spokes gamma-tubulin ring complex formed by the Candida albicans gamma-tubulin small complex in complex with Spc72 and Stu2
Sample
  • Complex: Full gamma-tubulin ring complex composed of the Candida albicans gamma-tubulin small complex in complex with Spc72 CM1
    • Protein or peptide: Tubulin gamma chain
    • Protein or peptide: Spindle pole body component
    • Protein or peptide: Spc98p
    • Protein or peptide: Mto2p-binding domain-containing protein
Keywordscytoskeleton / microtubule / microtubule nucleation / complex / template / cap / gamma-tubulin / gamma-tubulin ring complex / gamma-tubulin small complex / Spc72 / CM1 / CM1 motif / GCP2 / GCP3 / Spc97 / Spc98 / Candida / albicans / CELL CYCLE / gamma-TuRC / gamma-TuSC / yeast / fungi
Function / homology
Function and homology information


gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle pole body / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle / spindle pole / mitotic cell cycle / microtubule ...gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle pole body / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle / spindle pole / mitotic cell cycle / microtubule / GTP binding / cytoplasm
Similarity search - Function
Gamma tubulin / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain ...Gamma tubulin / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / 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
Similarity search - Domain/homology
Spindle pole body component / Tubulin gamma chain / Spindle pole body component / Mto2p-binding domain-containing protein
Similarity search - Component
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsVermeulen BJA / Pfeffer S
Funding support Germany, 6 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Schi 295/4-4 Germany
German Research Foundation (DFG)PF 963/1-4 Germany
German Research Foundation (DFG)PF 963/4-1 Germany
Other private
German Research Foundation (DFG)INST 35/1314-1 FUGG Germany
German Research Foundation (DFG)INST 35/1134-1 FUGG Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the interplay between microtubule polymerases, γ-tubulin complexes and their receptors.
Authors: Anjun Zheng / Bram J A Vermeulen / Martin Würtz / Annett Neuner / Nicole Lübbehusen / Matthias P Mayer / Elmar Schiebel / Stefan Pfeffer /
Abstract: The γ-tubulin ring complex (γ-TuRC) is a structural template for controlled nucleation of microtubules from α/β-tubulin heterodimers. At the cytoplasmic side of the yeast spindle pole body, the ...The γ-tubulin ring complex (γ-TuRC) is a structural template for controlled nucleation of microtubules from α/β-tubulin heterodimers. At the cytoplasmic side of the yeast spindle pole body, the CM1-containing receptor protein Spc72 promotes γ-TuRC assembly from seven γ-tubulin small complexes (γ-TuSCs) and recruits the microtubule polymerase Stu2, yet their molecular interplay remains unclear. Here, we determine the cryo-EM structure of the Candida albicans cytoplasmic nucleation unit at 3.6 Å resolution, revealing how the γ-TuRC is assembled and conformationally primed for microtubule nucleation by the dimerised Spc72 CM1 motif. Two coiled-coil regions of Spc72 interact with the conserved C-terminal α-helix of Stu2 and thereby position the α/β-tubulin-binding TOG domains of Stu2 in the vicinity of the microtubule assembly site. Collectively, we reveal the function of CM1 motifs in γ-TuSC oligomerisation and the recruitment of microtubule polymerases to the γ-TuRC.
History
DepositionOct 31, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51972.png

Downloads & links

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Map

FileDownload / File: emd_51972.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map for cryo-EM reconstruction of a full, 14-spokes gamma-tubulin ring complex formed by the Candida albicans gamma-tubulin small complex in complex with Spc72 and Stu2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00502
Minimum - Maximum-0.024658285 - 0.060033344
Average (Standard dev.)0.0003299226 (±0.0020402346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 547.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Multi-body refinement, body 3 for cryo-EM reconstruction of...

Fileemd_51972_additional_1.map
AnnotationMulti-body refinement, body 3 for cryo-EM reconstruction of a full, 14-spokes gamma-tubulin ring complex formed by the Candida albicans gamma-tubulin small complex in complex with Spc72 and Stu2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Multi-body refinement, body 1 for cryo-EM reconstruction of...

Fileemd_51972_additional_2.map
AnnotationMulti-body refinement, body 1 for cryo-EM reconstruction of a full, 14-spokes gamma-tubulin ring complex formed by the Candida albicans gamma-tubulin small complex in complex with Spc72 and Stu2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Multi-body refinement, body 2 for cryo-EM reconstruction of...

Fileemd_51972_additional_3.map
AnnotationMulti-body refinement, body 2 for cryo-EM reconstruction of a full, 14-spokes gamma-tubulin ring complex formed by the Candida albicans gamma-tubulin small complex in complex with Spc72 and Stu2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 for the cryo-EM reconstruction of...

Fileemd_51972_half_map_1.map
AnnotationHalf map 1 for the cryo-EM reconstruction of a full, 14-spokes gamma-tubulin ring complex formed by the Candida albicans gamma-tubulin small complex in complex with Spc72 and Stu2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for the cryo-EM reconstruction of...

Fileemd_51972_half_map_2.map
AnnotationHalf map 2 for the cryo-EM reconstruction of a full, 14-spokes gamma-tubulin ring complex formed by the Candida albicans gamma-tubulin small complex in complex with Spc72 and Stu2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full gamma-tubulin ring complex composed of the Candida albicans ...

EntireName: Full gamma-tubulin ring complex composed of the Candida albicans gamma-tubulin small complex in complex with Spc72 CM1
Components
  • Complex: Full gamma-tubulin ring complex composed of the Candida albicans gamma-tubulin small complex in complex with Spc72 CM1
    • Protein or peptide: Tubulin gamma chain
    • Protein or peptide: Spindle pole body component
    • Protein or peptide: Spc98p
    • Protein or peptide: Mto2p-binding domain-containing protein

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Supramolecule #1: Full gamma-tubulin ring complex composed of the Candida albicans ...

SupramoleculeName: Full gamma-tubulin ring complex composed of the Candida albicans gamma-tubulin small complex in complex with Spc72 CM1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candida albicans (yeast)

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Macromolecule #1: Tubulin gamma chain

MacromoleculeName: Tubulin gamma chain / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 56.228242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPGETITLQV GQCGNQVGLQ YWQQLATEHG IQSDGSSTPY PKDINDLQLQ ELNNSGSSPQ SYPQQTKPNG KYRNDHPELF FTLSDSNTY TPRSILIDME PSVIAKSTSA LPMFNPRNVH LSNQGNGAAN NWINGYKYGT EEEETLLNLI DREVDKCDNL S NFQLFHSV ...String:
MPGETITLQV GQCGNQVGLQ YWQQLATEHG IQSDGSSTPY PKDINDLQLQ ELNNSGSSPQ SYPQQTKPNG KYRNDHPELF FTLSDSNTY TPRSILIDME PSVIAKSTSA LPMFNPRNVH LSNQGNGAAN NWINGYKYGT EEEETLLNLI DREVDKCDNL S NFQLFHSV AGGTGSGVGS KMLEVISDRY GHKKLLNTFS IFPSNEDTSD VVVQPYNTIL TLKRLIDYSD ATFVFHNDSL NR IENILFN NNSNIQHDDN DLFLGANKLI ALVSASVSNP LRFPGYMYSS MESIVSNLIP TPDLKFLTSS IAPFSTQKHN YLN EYDMLL ELSNDRYKTN RVSGDTSYIS MLNYLIGDNL DQREIRKGIL KSQQRISFVP WVARSVLVVH GKKSPYLKNT NLEG IQVTN NTSMIDVFTK ILKQFDLLIK RKAYLNRYYS SVEEENEVME MFNESRESVK SIIDEYKACK EITYLDDDDE DDLED GGGN GNGYNNIDDA DMGI

UniProtKB: Tubulin gamma chain

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Macromolecule #2: Spindle pole body component

MacromoleculeName: Spindle pole body component / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 104.692742 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHDYD IPTTENLYFQ GAMDPMNTFS SPPNVIREYN DSTYQSPLNS QFHQSPFLQT QSPDYVSLRE EEDDNNDKNL DIMSSCIVD SVIYKSQKIA GPLLSQISNL NIQQALIIRE LLFTLLGHEG HYIQYSKRYD PTSQISRIEG PDYKIAKNLD I SLKVITKK ...String:
MHHHHHHDYD IPTTENLYFQ GAMDPMNTFS SPPNVIREYN DSTYQSPLNS QFHQSPFLQT QSPDYVSLRE EEDDNNDKNL DIMSSCIVD SVIYKSQKIA GPLLSQISNL NIQQALIIRE LLFTLLGHEG HYIQYSKRYD PTSQISRIEG PDYKIAKNLD I SLKVITKK LVKFGKFYSG LKSFIQVFDN NKFGKIVQKF CSEVRKFLSS YQQVLINVEH EFKFNKNFNL NMLDSLLHQE IS NEMTHLY QIGIEISRIT EERQKMSQAE IMGNFEPTTL ANTSMNGINS EPNLYYGKFD CCKGGLLLQV IQERMVYYKG DPT SLDFLT QLFDIVSSDY IGMLNQWLLE GVINDPFDEF MIREKRVPDS FMEIFQSKSE YYWNELFLIK IDGLLNQFQN STIQ SKILN TGKYLNIFKR CTGLHNFESL KEKLTTITSL AAPDLELKID EFYHRANKML MKLLFDGYNF PSVVNIFQRL FLFAD SFQI DNFIDSTFSE LKRGKLKISV SRLQKQYDDI FKEKIENKVG VRPSVYDVLK KNQKLSVTSE SLYKVVEELM EKNSDY LIS DNNLRGIFHR VASLRDDSRL TISSTADSAT ENVKDEPTIT SVDLTIPLPF PLNLVLNQQL SYQYEIMFKL LINIKFI SK YNSSNWQEMN YSKIWTNSHF NSSVKKWILR CRVLHSRICS FIHELENYIV HDVIEHNFEE IKNLIHTTAT NLATSELG S DINDEGDNIF NGSLIRGTFN NNSIFDSKVH KHRTTTYVEG ISTVEQLIQK FLDYSSTLLN DSLLTREESL RQLRKMLDF IFHFNNYIVQ VKKVLVLLNH ELFNEYSKEF PTKFEKPMDQ ESIDKRFANL SDTFLMQYEK FGENLVTFLA TIKQVGEREN QGLLELSNR LELCFPE

UniProtKB: Spindle pole body component

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Macromolecule #3: Spc98p

MacromoleculeName: Spc98p / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 95.318438 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHDYD IPTTENLYFQ GAMDPMALNK VQLIKLYSNR LVKSLVPVEF GEAFIQSIIN DLQTTLLNTS SEEQNLSIII NKLKMQFLS NNLKNEWVEF QNIVNSLSKF KSLDQICNYL AFLDALRDEK PEDILSTSTA SLSPGKQNVM INTVNTALTL S QLIEPYYD ...String:
MHHHHHHDYD IPTTENLYFQ GAMDPMALNK VQLIKLYSNR LVKSLVPVEF GEAFIQSIIN DLQTTLLNTS SEEQNLSIII NKLKMQFLS NNLKNEWVEF QNIVNSLSKF KSLDQICNYL AFLDALRDEK PEDILSTSTA SLSPGKQNVM INTVNTALTL S QLIEPYYD TLSEQTILTY LPYTMLGSDS KIFTFSNNYT RLEIPKDINN SFSSLLREVF EFAILYKQLA IVVDRYKGTL VS AIKTAYI AILEAQLNKY VNDINNIFNN KPNSILVVYN SIFPWISILR FLYRVSNRLN RLDGYEFLTF IYSFTNHGDP KIR GIAVTA FTEVVKPYYN IVEHWIVKGE LIDNNNEFFI IFDQEQNEFN SIIKLLPKKI PAFIKSSDKI FQIGKTLIFL NKYC RELKW VNQYNVKYSA ILFNNHQGLA SMTTNEMIKL IDSQYNEILT FLTQIIQGNN KLFTHVYNFK RFYFMETNDF IDAIM VKGK DVFNESSVNI SSTYLRKVLQ DAIQISSVKN FEYVDRLDSR VLNPQHGNLG WESFTIEYKI DDLPMSYLFE GHQHLQ YLK MFHFLWKLRQ LNNLLNWHFE MFNELNHNVV TKLSSRNRRP LAKSLSIITS IRFHFTQFLN ELIAYLSYDV IEENFQQ HI VRKLFYNKND QDLLLNKSFM NLSEIDPNND LPKFNVNLLT IDELVELHGT YIDSIINSSL LNEKLKGNET NISYIDQI F NILQTIFNFI NTSQEFYSLV CTFGLLVRSD SNANKIELEQ DQEDLEFQLH KIKRKIYKDI YQHDYKRQLN DLKNDLNRD YNLKDLSKLL

UniProtKB: Spindle pole body component

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Macromolecule #4: Mto2p-binding domain-containing protein

MacromoleculeName: Mto2p-binding domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 70.622578 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSNLSINESN DNSNVSILSN KSGAQSSTNS SPNLIVFKQP EDLSIQLQQQ QQGTQEDTPE EEEEEEEEME QITQLEVQQE NQPDTLSSS PFISRPNSPL DDIIRPQGTS SPSLTIRDSY SSQVDINISN LHKSLNEMRL STDPVDNNNN NNKVNKNNPT N SDISNDDI ...String:
MSNLSINESN DNSNVSILSN KSGAQSSTNS SPNLIVFKQP EDLSIQLQQQ QQGTQEDTPE EEEEEEEEME QITQLEVQQE NQPDTLSSS PFISRPNSPL DDIIRPQGTS SPSLTIRDSY SSQVDINISN LHKSLNEMRL STDPVDNNNN NNKVNKNNPT N SDISNDDI ITIDNLTPSR IQPKNISPWR QFRPTLRGSP ESTPRSLFQN KPNLKFNNGL SPTNGSRDMV TNNIATTTKS RE EELNKRI VNYKIQLKLM KNFLQELIDR NNLDPHEFHT LLRRNNNNIM NNENNPLSTS LSQTSTLEIQ HQNLQIELDE ALE LNKQLY NKIETANKEI SDKDLQISNY ESRINLINYS VDELIYILIN EYDKNNYSHG GSNTTSPGKE TLQQSISAQL EVKL NVLKL ELMTRLDQSH QYNNKPHDLF TPPYTSSEYG VSTNNVANKN DLEGYIHIIE DLIKTVDELE LTCENYKANK NELQN QLVE QINESIRIKN NFQIMSNKFN QLRQSLSEKE NDKNLDEFSK NNHQQQQQQQ IQQLEQKLIE YEKCITILQD ELDQYK QPS DTTNTTNNNN NNNNNNNRSS YSSYNNHRNS SLNELNGSGS GSEQKLISEE DL

UniProtKB: Mto2p-binding domain-containing protein

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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: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 33781 / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 8261
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9h9r:
Full gamma-tubulin ring complex composed of the Candida albicans gamma-tubulin small complex in complex with Spc72 CM1

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