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- PDB-9ya3: Cryo-EM structure of the apical region of subpellicular microtubu... -

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Basic information

Entry
Database: PDB / ID: 9ya3
TitleCryo-EM structure of the apical region of subpellicular microtubule (SPMT) from Toxoplasma gondii (8-nm repeat)
Components
  • Microtubule associated protein SPM1
  • TLAP2 (thioredoxin-like associated protein), TGME49_232130
  • 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 / subpellicular microtubule / SPMT
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 / WD40/YVTN repeat-like-containing domain 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: 3.3 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: Zeng, J. / Fu, Y. / Qian, P. / Niu, Q. / Beatty, W.L. / Brown, A. / Sibley, L.D. / Zhang, R.
History
DepositionSep 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Microtubule associated protein SPM1
1: Microtubule associated protein SPM1
10: Microtubule associated protein SPM1
11: Microtubule associated protein SPM1
12: Microtubule associated protein SPM1
13: Microtubule associated protein SPM1
14: Microtubule associated protein SPM1
15: Microtubule associated protein SPM1
16: Microtubule associated protein SPM1
17: Microtubule associated protein SPM1
18: Microtubule associated protein SPM1
19: Microtubule associated protein SPM1
2: Microtubule associated protein SPM1
22: Microtubule associated protein SPM1
23: Microtubule associated protein SPM1
3: Microtubule associated protein SPM1
4: Microtubule associated protein SPM1
5: Microtubule associated protein SPM1
6: Microtubule associated protein SPM1
7: Microtubule associated protein SPM1
8: Microtubule associated protein SPM1
9: Microtubule associated protein SPM1
A: TLAP3 (apical cap protein AC5), TGME49_235380
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: TLAP3 (apical cap protein AC5), TGME49_235380
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: TLAP3 (apical cap protein AC5), TGME49_235380
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
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: TLAP4 (thioredoxin-like associated protein), TGME49_201760
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: TLAP4 (thioredoxin-like associated protein), TGME49_201760
F0: Tubulin alpha chain
F1: Tubulin beta chain
G: TLAP4 (thioredoxin-like associated protein), TGME49_201760
H: TLAP2 (thioredoxin-like associated protein), TGME49_232130
I: TLAP2 (thioredoxin-like associated protein), TGME49_232130
J: TLAP2 (thioredoxin-like associated protein), TGME49_232130
K: TLAP2 (thioredoxin-like associated protein), TGME49_232130
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)4,579,472186
Polymers4,553,714108
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, 108 molecules 0110111213141516171819222233456789ABCA0A2A4A6A8...

#1: Protein ...
Microtubule associated protein SPM1


Mass: 38845.750 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K285
#2: Protein TLAP3 (apical cap protein AC5), TGME49_235380


Mass: 65286.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A151H4L4
#3: Protein ...
Tubulin alpha chain / Alpha-tubulin / 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
#4: 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
#5: Protein TLAP4 (thioredoxin-like associated protein), TGME49_201760


Mass: 37360.230 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K913
#6: Protein
TLAP2 (thioredoxin-like associated protein), TGME49_232130


Mass: 47924.449 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YLA3
#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-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
#10: 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
#11: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225207 / Symmetry type: POINT

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