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- PDB-9ya2: Cryo-EM structure of intraconoidal microtubule 1 (ICMT1) from Tox... -

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Basic information

Entry
Database: PDB / ID: 9ya2
TitleCryo-EM structure of intraconoidal microtubule 1 (ICMT1) from Toxoplasma gondii (8-nm repeat)
Components
  • ICMAP2, TGME49_224700
  • Microtubule associated protein SPM1
  • TLAP3 (apical cap protein AC5), TGME49_235380
  • TLAP4 (thioredoxin-like associated protein), TGME49_201760
  • TRXL1, TGME49_232410
  • TRXL2, TGME49_225790
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / Tubulin / Microtubule / Microtubule Inner Protein / Microtubule-associated Protein / Toxoplasma gondii / conoid / conoid fiber / intraconoidal microtubule / ICMT
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / negative regulation of Wnt signaling pathway / microtubule-based process / negative regulation of protein ubiquitination / structural constituent of cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton / hydrolase activity ...thioredoxin-disulfide reductase (NADPH) activity / negative regulation of Wnt signaling pathway / microtubule-based process / negative regulation of protein ubiquitination / structural constituent of cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton / hydrolase activity / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Stabilizer of axonemal microtubules 1/2 / Thioredoxin-like / Thioredoxin-like fold / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain ...Stabilizer of axonemal microtubules 1/2 / Thioredoxin-like / Thioredoxin-like fold / Alpha tubulin / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Uncharacterized protein / Uncharacterized protein / PDI family protein / Microtubule associated protein SPM1 / Uncharacterized protein / Tubulin beta chain / Tubulin alpha chain / PDI family protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsZeng, J. / Zhang, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI179885 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Atomic models of the Toxoplasma cell invasion machinery.
Authors: Jianwei Zeng / Yong Fu / Pengge Qian / Wei Huang / Qingwei Niu / Wandy L Beatty / Alan Brown / L David Sibley / Rui Zhang /
Abstract: Apicomplexan parasites, responsible for toxoplasmosis, cryptosporidiosis and malaria, invade host cells through a unique gliding motility mechanism powered by actomyosin motors and a dynamic ...Apicomplexan parasites, responsible for toxoplasmosis, cryptosporidiosis and malaria, invade host cells through a unique gliding motility mechanism powered by actomyosin motors and a dynamic organelle called the conoid. Here, using cryo-electron microscopy, we determined structures of four essential complexes of the Toxoplasma gondii conoid: the preconoidal P2 ring, tubulin-based conoid fibers, and the subpellicular and intraconoidal microtubules. Our analysis identified 40 distinct conoid proteins, several of which are essential for parasite lytic growth, as revealed through genetic disruption studies. Comparative analysis of the tubulin-containing complexes sheds light on their functional specialization by microtubule-associated proteins, while the structure of the preconoidal ring pinpoints the site of actin polymerization and initial translocation, enhancing our mechanistic understanding of gliding motility and, therefore, parasite invasion.
History
DepositionSep 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2025Group: Data collection / Database references / Category: citation_author / em_admin / Item: _em_admin.last_update
Revision 1.1Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation_author / em_admin / Data content type: EM metadata / Item: _em_admin.last_update
Revision 1.2Dec 24, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule associated protein SPM1
A0: Tubulin alpha chain
A1: Tubulin beta chain
A2: Tubulin alpha chain
A3: Tubulin beta chain
A4: Tubulin alpha chain
A5: Tubulin beta chain
A6: Tubulin alpha chain
A7: Tubulin beta chain
A8: Tubulin alpha chain
A9: Tubulin beta chain
B: Microtubule associated protein SPM1
B0: Tubulin alpha chain
B1: Tubulin beta chain
B2: Tubulin alpha chain
B3: Tubulin beta chain
B4: Tubulin alpha chain
B5: Tubulin beta chain
B6: Tubulin alpha chain
B7: Tubulin beta chain
B8: Tubulin alpha chain
B9: Tubulin beta chain
C: Microtubule associated protein SPM1
C0: Tubulin alpha chain
C1: Tubulin beta chain
C2: Tubulin alpha chain
C3: Tubulin beta chain
C4: Tubulin alpha chain
C5: Tubulin beta chain
C6: Tubulin alpha chain
C7: Tubulin beta chain
C8: Tubulin alpha chain
C9: Tubulin beta chain
D: Microtubule associated protein SPM1
D0: Tubulin alpha chain
D1: Tubulin beta chain
D2: Tubulin alpha chain
D3: Tubulin beta chain
D4: Tubulin alpha chain
D5: Tubulin beta chain
D6: Tubulin alpha chain
D7: Tubulin beta chain
D8: Tubulin alpha chain
D9: Tubulin beta chain
E: Microtubule associated protein SPM1
E0: Tubulin alpha chain
E1: Tubulin beta chain
E2: Tubulin alpha chain
E3: Tubulin beta chain
E4: Tubulin alpha chain
E5: Tubulin beta chain
E6: Tubulin alpha chain
E7: Tubulin beta chain
E8: Tubulin alpha chain
E9: Tubulin beta chain
F: Microtubule associated protein SPM1
F0: Tubulin alpha chain
F1: Tubulin beta chain
G: Microtubule associated protein SPM1
H: Microtubule associated protein SPM1
I: Microtubule associated protein SPM1
J: Microtubule associated protein SPM1
K: Microtubule associated protein SPM1
L: ICMAP2, TGME49_224700
M: ICMAP2, TGME49_224700
N: ICMAP2, TGME49_224700
O: TLAP3 (apical cap protein AC5), TGME49_235380
P: TLAP3 (apical cap protein AC5), TGME49_235380
Q: ICMAP2, TGME49_224700
R: TLAP4 (thioredoxin-like associated protein), TGME49_201760
S: TLAP4 (thioredoxin-like associated protein), TGME49_201760
T: TLAP4 (thioredoxin-like associated protein), TGME49_201760
U: TLAP4 (thioredoxin-like associated protein), TGME49_201760
V: ICMAP2, TGME49_224700
W: ICMAP2, TGME49_224700
a: TRXL1, TGME49_232410
b: TRXL1, TGME49_232410
c: TRXL1, TGME49_232410
d: TRXL1, TGME49_232410
e: TRXL1, TGME49_232410
f: TRXL1, TGME49_232410
g: TRXL1, TGME49_232410
h: TRXL1, TGME49_232410
i: TRXL1, TGME49_232410
j: TRXL1, TGME49_232410
k: TRXL2, TGME49_225790
l: TRXL2, TGME49_225790
m: TRXL1, TGME49_232410
n: TRXL1, TGME49_232410
o: TRXL1, TGME49_232410
p: TRXL1, TGME49_232410
q: TRXL1, TGME49_232410
r: TRXL1, TGME49_232410
s: TRXL1, TGME49_232410
t: TRXL1, TGME49_232410
u: TRXL1, TGME49_232410
v: TRXL1, TGME49_232410
w: TRXL1, TGME49_232410
x: TRXL1, TGME49_232410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,030,084177
Polymers5,004,32699
Non-polymers25,75878
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 8 types, 99 molecules ABCDEFGHIJKA0A2A4A6A8B0B2B4B6B8C0C2C4C6C8D0D2D4D6...

#1: Protein
Microtubule associated protein SPM1 / TGME49_263520


Mass: 38845.750 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K285
#2: Protein ...
Tubulin alpha chain / Alpha-tubulin TUBA1 / TGME49_316400


Mass: 50166.645 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: P10873
#3: Protein ...
Tubulin beta chain / beta tubulin / TGME49_266960


Mass: 50119.121 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: I7BFC9
#4: Protein
ICMAP2, TGME49_224700


Mass: 182923.125 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A086KMN2
#5: Protein TLAP3 (apical cap protein AC5), TGME49_235380


Mass: 65286.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A151H4L4
#6: Protein
TLAP4 (thioredoxin-like associated protein), TGME49_201760


Mass: 37360.230 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K913
#7: Protein ...
TRXL1, TGME49_232410 / PDI family protein / Putative PDI-like protein


Mass: 24939.332 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: Q8MPF4
#8: Protein TRXL2, TGME49_225790 / PDI family protein / TrxL2


Mass: 21687.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K232

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Non-polymers , 3 types, 78 molecules

#9: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#10: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: conoid fiber from Toxoplasma gondii (24-nm repeat) / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 5000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57592 / Symmetry type: POINT

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