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Yorodumi- EMDB-26019: Subpellicular microtubule from detergent-extract Toxoplasma gondi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26019 | ||||||||||||||||||
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Title | Subpellicular microtubule from detergent-extract Toxoplasma gondii cells | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Function / homology | Function and homology information protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / 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 binding / microtubule / hydrolase activity / GTPase activity ...protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / 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 binding / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 6.7 Å | ||||||||||||||||||
Authors | Sun SY / Pintilie GD / Chen M / Chiu W | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 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 | emd_26019.map.gz | 6.4 MB | EMDB map data format | |
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Header (meta data) | emd-26019-v30.xml emd-26019.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_26019.png | 106.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26019 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26019 | HTTPS FTP |
-Validation report
Summary document | emd_26019_validation.pdf.gz | 385.3 KB | Display | EMDB validaton report |
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Full document | emd_26019_full_validation.pdf.gz | 384.9 KB | Display | |
Data in XML | emd_26019_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_26019_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26019 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26019 | HTTPS FTP |
-Related structure data
Related structure data | 7tnsMC 7tnqC 7tntC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26019.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 2.0715 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : microtubule complex of alpha-tubulin and beta-tubulin with intra-...
Entire | Name: microtubule complex of alpha-tubulin and beta-tubulin with intra-lumenal proteins |
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Components |
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-Supramolecule #1: microtubule complex of alpha-tubulin and beta-tubulin with intra-...
Supramolecule | Name: microtubule complex of alpha-tubulin and beta-tubulin with intra-lumenal proteins type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Toxoplasma gondii (eukaryote) / Strain: ME49 |
-Macromolecule #1: Microtubule associated protein SPM1
Macromolecule | Name: Microtubule associated protein SPM1 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (eukaryote) / Strain: ATCC 50611 / Me49 |
Molecular weight | Theoretical: 38.817699 KDa |
Sequence | String: MSGGNSNTPK KLPSEEGSDY GYPQKPQKYL PKSEQAEPDY SACCKGNDAY KGASHGTVQF SHPEEAQKYA GAAAGAETIQ RGRERVAAD RQPRAAGDVP ARRLHLSDVD EAHRGQSPSR HPGYCVEELC TCGMHKCIPS RAPVPFTGST QYRQEFVPKP L PPPTQVSQ ...String: MSGGNSNTPK KLPSEEGSDY GYPQKPQKYL PKSEQAEPDY SACCKGNDAY KGASHGTVQF SHPEEAQKYA GAAAGAETIQ RGRERVAAD RQPRAAGDVP ARRLHLSDVD EAHRGQSPSR HPGYCVEELC TCGMHKCIPS RAPVPFTGST QYRQEFVPKP L PPPTQVSQ VTLPPSLPFE AESSYRTEFV AKPLPPPAKF SEVKLPPTLP FHGESAYRTD YVPKPLPEVA KPVEVKLPPT LP FNAQSCY RSEYVAKPLP PPVQTAEVKL PPSLPFEGST HYRDEFQVKP LPPATKVTEV KLPPSLPFDA TSMYRSDYVA KSN PICPVS KLPQYPAATY PQNHVFWDPD TKQWY |
-Macromolecule #2: Tubulin alpha chain
Macromolecule | Name: Tubulin alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (eukaryote) / Strain: ME49 |
Molecular weight | Theoretical: 50.166645 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 GIETAEGEGE EEGYGDEY |
-Macromolecule #3: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (eukaryote) / Strain: ATCC 50611 / Me49 |
Molecular weight | Theoretical: 50.119121 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 QDATAEEEGE FDEEEGEMGA EEGA |
-Macromolecule #4: PDI family protein
Macromolecule | Name: PDI family protein / type: protein_or_peptide / ID: 4 / Number of copies: 24 / Enantiomer: LEVO / EC number: protein-disulfide reductase |
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Source (natural) | Organism: Toxoplasma gondii (eukaryote) / Strain: ATCC 50611 / Me49 |
Molecular weight | Theoretical: 24.939332 KDa |
Sequence | String: MSQPVFASPL NVEKRRLNEE RALMQAQKAG GEGVNIQLPP NYGDMDLILF PEGSLKNSNN TVIPQSHLKG KSVALYFADG ADPKCASLL PFLLNYYRTM NEGGANQKIE IIFVSLDRDR EAFESHRAHM PWLSIDLENP LTEILKRHFR VMKEYEVPTY G YGSRTGVP ...String: MSQPVFASPL NVEKRRLNEE RALMQAQKAG GEGVNIQLPP NYGDMDLILF PEGSLKNSNN TVIPQSHLKG KSVALYFADG ADPKCASLL PFLLNYYRTM NEGGANQKIE IIFVSLDRDR EAFESHRAHM PWLSIDLENP LTEILKRHFR VMKEYEVPTY G YGSRTGVP SVIVIGSDGR EAQFLPICSG LEEGDRALLR WDWRNTKFAS DQFHVRPTLL EQ |
-Macromolecule #5: PDI family protein
Macromolecule | Name: PDI family protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (eukaryote) / Strain: ATCC 50611 / Me49 |
Molecular weight | Theoretical: 21.687934 KDa |
Sequence | String: MLAADCFFGP DVVKRTQQGN YVPVRPDHFA GVSVALFFAK AGHSKCAQIV PVVRQFYKTT NFSGEKAVIE IIYVSLDKDE QDFERVRAL MPWCSVEYKS CLRKKLIERY RVPNGELAFG TVRIPSTAIP LLIVIGPNGE EAGRMNFQQS DEFVLQRWDY R FNKWPGSA QRLRTLNDAT DPWKKRLPQN V |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | filament |
-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 |
-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 electron dose: 4.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 80.0 Å Applied symmetry - Helical parameters - Δ&Phi: 27.7 ° Applied symmetry - Helical parameters - Axial symmetry: C13 (13 fold cyclic) Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 39122 |
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Extraction | Number tomograms: 90 / Number images used: 39122 |
CTF correction | Software - Name: EMAN2 |
Final angle assignment | Type: OTHER |