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- EMDB-26020: The tubulin-based conoid from detergent-extract Toxoplasma gondii... -
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Open data
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Basic information
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Title | The tubulin-based conoid from detergent-extract Toxoplasma gondii cells | ||||||||||||||||||
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Function / homology | ![]() Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.3 Å | ||||||||||||||||||
![]() | Sun SY / Pintilie GD / Chen M / Chiu W | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-ET of parasites gives subnanometer insight into tubulin-based structures. Authors: Stella Y Sun / Li-Av Segev-Zarko / Muyuan Chen / Grigore D Pintilie / Michael F Schmid / Steven J Ludtke / John C Boothroyd / Wah Chiu / ![]() Abstract: Tubulin is a conserved protein that polymerizes into different forms of filamentous structures in , an obligate intracellular parasite in the phylum Apicomplexa. Two key tubulin-containing ...Tubulin is a conserved protein that polymerizes into different forms of filamentous structures in , an obligate intracellular parasite in the phylum Apicomplexa. Two key tubulin-containing cytoskeletal components are subpellicular microtubules (SPMTs) and conoid fibrils (CFs). The SPMTs help maintain shape and gliding motility, while the CFs are implicated in invasion. Here, we use cryogenic electron tomography to determine the molecular structures of the SPMTs and CFs in vitrified intact and detergent-extracted parasites. Subvolume densities from detergent-extracted parasites yielded averaged density maps at subnanometer resolutions, and these were related back to their architecture in situ. An intralumenal spiral lines the interior of the 13-protofilament SPMTs, revealing a preferred orientation of these microtubules relative to the parasite's long axis. Each CF is composed of nine tubulin protofilaments that display a comma-shaped cross-section, plus additional associated components. Conoid protrusion, a crucial step in invasion, is associated with an altered pitch of each CF. The use of basic building blocks of protofilaments and different accessory proteins in one organism illustrates the versatility of tubulin to form two distinct types of assemblies, SPMTs and CFs. | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
Images | ![]() | 101 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tntMC ![]() 7tnqC ![]() 7tnsC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 3.534 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : a conoid complex of tubulin with other protein components
Entire | Name: a conoid complex of tubulin with other protein components |
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Components |
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-Supramolecule #1: a conoid complex of tubulin with other protein components
Supramolecule | Name: a conoid complex of tubulin with other protein components type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Tubulin alpha chain
Macromolecule | Name: Tubulin alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 48.421031 KDa |
Sequence | String: MREVISIHVG QAGIQIGNAC WELFCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCVFLDL EPTVVDEVRT GTYRHLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLSL DRIRKLADNC TGLQGFLMFN AVGGGTGSGL GCLLLERLSV D YGKKSKLN ...String: MREVISIHVG QAGIQIGNAC WELFCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCVFLDL EPTVVDEVRT GTYRHLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLSL DRIRKLADNC TGLQGFLMFN AVGGGTGSGL GCLLLERLSV D YGKKSKLN FCSWPSPQVS TAVVEPYNSV LSTHSLLEHT DVAVMLDNEA IYDICRRNLD IERPTYTNLN RLIAQVISSL TA SLRFDGA LNVDVTEFQT NLVPYPRIHF MLSSYAPIIS AEKAYHEQLS VAEITNSAFE PASMMAKCDP RHGKYMACCL MYR GDVVPK DVNAAVATIK TKRTIQFVDW CPTGFKCGIN YQPPTVVPGG DLAKVMRAVC MISNSTAIAE VFSRMDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDYEEV GI |
-Macromolecule #2: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 47.70582 KDa |
Sequence | String: MREIVHVQGG QCGNQIGAKF WEVISDEHGI DPTGTYCGDS DLQLERINVF YNEATGGRFV PRAILMDLEP GTMDSVRAGP FGQLFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAEGCDC LQGFQITHSL GGGTGSGMGT LLISKVREEY P DRIMETFS ...String: MREIVHVQGG QCGNQIGAKF WEVISDEHGI DPTGTYCGDS DLQLERINVF YNEATGGRFV PRAILMDLEP GTMDSVRAGP FGQLFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAEGCDC LQGFQITHSL GGGTGSGMGT LLISKVREEY P DRIMETFS VFPSPKVSDT VVEPYNATLS VHQLVENADE VQVIDNEALY DICFRTLKLT TPTYGDLNHL VSAAMSGVTC CL RFPGQLN SDLRKLAVNL IPFPRLHFFL IGFAPLTSRG SQQYRALSVP ELTQQMFDAK NMMCASDPRH GRYLTASAMF RGR MSTKEV DEQMLNVQNK NSSYFVEWIP NNMKSSVCDI PPKGLKMSVT FVGNSTAIQE MFKRVSDQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY Q |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.2 / Details: Phosphate Buffered Saline |
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Grid | Model: Homemade / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 1.2 sec. / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen 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
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 29524 |
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Extraction | Number tomograms: 126 / Number images used: 29524 |
CTF correction | Software - Name: EMAN2 |
Final angle assignment | Type: OTHER |