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- PDB-7tnt: The tubulin-based conoid from detergent-extract Toxoplasma gondii... -

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Basic information

Entry
Database: PDB / ID: 7tnt
TitleThe tubulin-based conoid from detergent-extract Toxoplasma gondii cells
Components
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL INVASION / parasites / Toxoplasma gondii / cytoskeleton / conoid / tubulin
Function / homology
Function and homology information


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
Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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-beta mRNA autoregulation signal. / Alpha tubulin / 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
Similarity search - Domain/homology
Tubulin beta chain / Tubulin alpha chain
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.3 Å
AuthorsSun, S.Y. / Pintilie, G.D. / Chen, M. / Chiu, W.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD021600 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM121203 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R21MH125285-01A1 United States
CitationJournal: 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
DepositionJan 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2A: Tubulin alpha chain
2B: Tubulin alpha chain
2C: Tubulin alpha chain
2D: Tubulin alpha chain
2E: Tubulin alpha chain
2F: Tubulin alpha chain
2G: Tubulin alpha chain
2H: Tubulin alpha chain
2I: Tubulin alpha chain
3A: Tubulin beta chain
3B: Tubulin beta chain
3C: Tubulin beta chain
3D: Tubulin beta chain
3E: Tubulin beta chain
3F: Tubulin beta chain
3G: Tubulin beta chain
3H: Tubulin beta chain
3I: Tubulin beta chain
4A: Tubulin alpha chain
4B: Tubulin alpha chain
4C: Tubulin alpha chain
4D: Tubulin alpha chain
4E: Tubulin alpha chain
4F: Tubulin alpha chain
4G: Tubulin alpha chain
4H: Tubulin alpha chain
4I: Tubulin alpha chain
5A: Tubulin beta chain
5B: Tubulin beta chain
5C: Tubulin beta chain
5D: Tubulin beta chain
5E: Tubulin beta chain
5F: Tubulin beta chain
5G: Tubulin beta chain
5H: Tubulin beta chain
5I: Tubulin beta chain


Theoretical massNumber of molelcules
Total (without water)1,730,28336
Polymers1,730,28336
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Tubulin alpha chain / Alpha-tubulin


Mass: 48421.031 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / Strain: ME49 / References: UniProt: P10873
#2: Protein
Tubulin beta chain


Mass: 47705.820 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / Strain: ATCC 50611 / Me49 / References: UniProt: A0A125YWG5
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: a conoid complex of tubulin with other protein components
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Toxoplasma gondii (eukaryote) / Strain: ME49
Buffer solutionpH: 7.2 / Details: Phosphate Buffered Saline
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Homemade
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.2 sec. / Electron dose: 3 e/Å2 / Avg electron dose per subtomogram: 96 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 6

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Processing

EM software
IDNameVersionCategory
4EMAN2CTF correction
7UCSF Chimera1.3model fitting
12EMAN23D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29524 / Algorithm: FOURIER SPACE / Symmetry type: POINT
EM volume selectionNum. of tomograms: 126 / Num. of volumes extracted: 29524
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7MIZ

7miz

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