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- PDB-9ya0: Cryo-EM structure of pre-conoid ring 2 (PCR P2 ring)from Toxoplas... -

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Basic information

Entry
Database: PDB / ID: 9ya0
TitleCryo-EM structure of pre-conoid ring 2 (PCR P2 ring)from Toxoplasma gondii
Components
  • (Calmodulin) x 2
  • CGP, TGME49_240380
  • FLM1, TGME49_271780
  • FLM2, TGME49_285990
  • Formin 1
  • ICAP16, TGME49_202120
  • MLC4, TGME49_294390
  • PCR10, TGME49_298010
  • PCR11, TGME49_209490
  • PCR12, TGME49_219070
  • PCR12, TGME49_292170
  • PCR13, TGME49_284620
  • PCR14, TGME49_311880
  • PCR15, TGME49_232560
  • PCR4, TGME49_201220
  • PCR5, TGME49_242320
  • Protein transport protein SEC23
  • Transport protein Sec24
  • myosin L, TGME49_291020
KeywordsSTRUCTURAL PROTEIN / Tubulin / Microtubule / Microtubule Inner Protein / Microtubule-associated Protein / Toxoplasma gondii / conoid / conoid fiber / pre-conoid ring / PCR / P2
Function / homology
Function and homology information


cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / COPII-coated vesicle cargo loading / COPII vesicle coat / myosin complex / cAMP-dependent protein kinase inhibitor activity / myosin II complex / cAMP-dependent protein kinase complex / microfilament motor activity / protein kinase A catalytic subunit binding ...cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / COPII-coated vesicle cargo loading / COPII vesicle coat / myosin complex / cAMP-dependent protein kinase inhibitor activity / myosin II complex / cAMP-dependent protein kinase complex / microfilament motor activity / protein kinase A catalytic subunit binding / endoplasmic reticulum exit site / cAMP binding / GTPase activator activity / actin filament organization / SNARE binding / methyltransferase activity / intracellular protein transport / actin filament binding / actin cytoskeleton organization / methylation / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / zinc ion binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
CLU domain / CLU domain containing protein / CLU central domain / : / Translation initiation factor eIF3 subunit 135 / Clueless (Clu) domain profile. / : / : / Protein transport protein Sec23 / : ...CLU domain / CLU domain containing protein / CLU central domain / : / Translation initiation factor eIF3 subunit 135 / Clueless (Clu) domain profile. / : / : / Protein transport protein Sec23 / : / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Sec23/Sec24 beta-sandwich domain / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / : / Filamin family / Gelsolin-like domain superfamily / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Tetratricopeptide repeat / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Ca2+ insensitive EF hand / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / EF hand / Gelsolin-like domain / Gelsolin repeat / Ankyrin repeats (many copies) / ADF-H/Gelsolin-like domain superfamily / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / EF-hand domain pair / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / SET domain superfamily / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Kinesin motor domain superfamily / : / PH domain profile. / Pleckstrin homology domain. / von Willebrand factor A-like domain superfamily / SKP1/BTB/POZ domain superfamily / Pleckstrin homology domain / RmlC-like jelly roll fold / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Leucine-rich repeat domain superfamily / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Tetratricopeptide-like helical domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GYF domain-containing protein / Protein transport protein SEC23 / B-box zinc finger domain-containing protein / Uncharacterized protein / Calmodulin / Putative transport protein Sec24 / Calmodulin / Zinc finger protein / Putative myosin light chain MLC4 / Formin 1 ...GYF domain-containing protein / Protein transport protein SEC23 / B-box zinc finger domain-containing protein / Uncharacterized protein / Calmodulin / Putative transport protein Sec24 / Calmodulin / Zinc finger protein / Putative myosin light chain MLC4 / Formin 1 / Cyclic nucleotide-binding domain-containing protein / Histone lysine methyltransferase, SET, putative / Filamin/ABP280 repeat-containing protein / Myosin head (Motor domain) domain-containing protein / Clu domain-containing protein / Leucine rich repeat-containing protein / CLU central domain-containing protein / PH domain-containing protein / Uncharacterized protein / Filamin/ABP280 repeat-containing protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 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 1.0Nov 19, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: PCR5, TGME49_242320
AB: PCR4, TGME49_201220
AC: PCR4, TGME49_201220
AD: PCR5, TGME49_242320
AE: PCR5, TGME49_242320
AF: PCR4, TGME49_201220
AG: PCR4, TGME49_201220
AH: PCR5, TGME49_242320
AI: PCR5, TGME49_242320
AJ: PCR4, TGME49_201220
AK: PCR4, TGME49_201220
AL: PCR5, TGME49_242320
BA: Formin 1
BB: Formin 1
BC: Formin 1
CA: Formin 1
CB: Formin 1
CC: Formin 1
CE: Formin 1
CF: Formin 1
CG: Formin 1
CI: Formin 1
CJ: Formin 1
CL: Formin 1
DA: PCR11, TGME49_209490
DB: PCR11, TGME49_209490
DC: PCR11, TGME49_209490
DD: PCR11, TGME49_209490
DE: PCR11, TGME49_209490
DF: PCR11, TGME49_209490
EA: CGP, TGME49_240380
EB: CGP, TGME49_240380
EC: CGP, TGME49_240380
FA: FLM1, TGME49_271780
FB: FLM1, TGME49_271780
FC: FLM1, TGME49_271780
FD: FLM1, TGME49_271780
FE: FLM1, TGME49_271780
FF: FLM1, TGME49_271780
GA: Transport protein Sec24
GB: Protein transport protein SEC23
GC: Transport protein Sec24
GD: Protein transport protein SEC23
GE: Transport protein Sec24
GF: Protein transport protein SEC23
GG: Transport protein Sec24
GH: Protein transport protein SEC23
GI: Transport protein Sec24
GJ: Protein transport protein SEC23
GK: Transport protein Sec24
GL: Protein transport protein SEC23
HA: FLM2, TGME49_285990
HB: FLM2, TGME49_285990
HC: FLM2, TGME49_285990
HD: FLM2, TGME49_285990
IA: PCR12, TGME49_292170
IB: PCR12, TGME49_292170
IC: PCR12, TGME49_292170
JA: PCR10, TGME49_298010
JB: PCR10, TGME49_298010
JC: PCR10, TGME49_298010
KA: PCR14, TGME49_311880
KB: PCR14, TGME49_311880
KC: PCR14, TGME49_311880
KE: PCR14, TGME49_311880
KF: PCR14, TGME49_311880
KG: PCR14, TGME49_311880
LA: ICAP16, TGME49_202120
LB: ICAP16, TGME49_202120
LC: ICAP16, TGME49_202120
LD: ICAP16, TGME49_202120
LE: ICAP16, TGME49_202120
LF: ICAP16, TGME49_202120
LG: ICAP16, TGME49_202120
LH: ICAP16, TGME49_202120
LI: ICAP16, TGME49_202120
LJ: ICAP16, TGME49_202120
LK: ICAP16, TGME49_202120
LL: ICAP16, TGME49_202120
LM: ICAP16, TGME49_202120
LN: ICAP16, TGME49_202120
LO: ICAP16, TGME49_202120
LP: ICAP16, TGME49_202120
MA: PCR12, TGME49_219070
MB: PCR12, TGME49_219070
MC: PCR12, TGME49_219070
MD: PCR12, TGME49_219070
ME: PCR12, TGME49_219070
MF: PCR12, TGME49_219070
MG: PCR12, TGME49_219070
MH: PCR12, TGME49_219070
MI: PCR12, TGME49_219070
MJ: PCR12, TGME49_219070
MK: PCR12, TGME49_219070
ML: PCR12, TGME49_219070
NA: myosin L, TGME49_291020
NB: myosin L, TGME49_291020
NC: myosin L, TGME49_291020
ND: myosin L, TGME49_291020
OA: PCR13, TGME49_284620
OB: PCR13, TGME49_284620
OC: PCR13, TGME49_284620
PA: PCR15, TGME49_232560
PB: PCR15, TGME49_232560
PC: PCR15, TGME49_232560
QA: MLC4, TGME49_294390
QB: MLC4, TGME49_294390
QC: MLC4, TGME49_294390
QD: MLC4, TGME49_294390
RA: Calmodulin
RB: Calmodulin
RC: Calmodulin
RD: Calmodulin
SA: Calmodulin
SB: Calmodulin
SC: Calmodulin
SD: Calmodulin


Theoretical massNumber of molelcules
Total (without water)23,832,884117
Polymers23,832,884117
Non-polymers00
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 , 20 types, 117 molecules AAADAEAHAIALABACAFAGAJAKBABBBCCACBCCCECFCGCICJCLDADBDCDDDEDF...

#1: Protein
PCR5, TGME49_242320 / B-box zinc finger domain-containing protein


Mass: 119326.812 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YZK2
#2: Protein
PCR4, TGME49_201220 / Zinc finger protein


Mass: 68040.531 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K7R7
#3: Protein
Formin 1 / FRM1 / TGME49_206430


Mass: 552604.500 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: D0V3Y0
#4: Protein
PCR11, TGME49_209490


Mass: 56836.012 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A151HGZ3
#5: Protein CGP, TGME49_240380 / Clu domain-containing protein


Mass: 545690.750 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F7I2
#6: Protein
FLM1, TGME49_271780 / Filamin/ABP280 repeat-containing protein


Mass: 303103.719 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F1N8
#7: Protein
Transport protein Sec24 / SEC24 / TGME49_277000


Mass: 108131.289 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JV06
#8: Protein
Protein transport protein SEC23 / SEC23 / TGME49_291680


Mass: 87697.195 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YTJ1
#9: Protein
FLM2, TGME49_285990 / Filamin/ABP280 repeat-containing protein


Mass: 131144.031 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GR55
#10: Protein PCR12, TGME49_292170 / Histone lysine methyltransferase / SET / putative


Mass: 175593.656 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F0I2
#11: Protein PCR10, TGME49_298010 / CLU central domain-containing protein


Mass: 261711.625 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8FEI7
#12: Protein
PCR14, TGME49_311880 / GYF domain-containing protein


Mass: 81526.453 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YI95
#13: Protein
ICAP16, TGME49_202120 / PH domain-containing protein


Mass: 147400.141 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GEJ5
#14: Protein
PCR12, TGME49_219070 / Cyclic nucleotide-binding domain-containing protein


Mass: 310184.094 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8EN17, cGMP-dependent protein kinase
#15: Protein
myosin L, TGME49_291020


Mass: 278088.031 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F3J9
#16: Protein PCR13, TGME49_284620 / Leucine rich repeat-containing protein


Mass: 254343.016 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8FB83
#17: Protein PCR15, TGME49_232560


Mass: 200557.844 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GK29
#18: Protein
MLC4, TGME49_294390 / Putative myosin light chain MLC4


Mass: 19716.730 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KI07
#19: Protein
Calmodulin / CAM1 / TGME49_246930


Mass: 19070.646 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JTN7
#20: Protein
Calmodulin / CAM4 / TGME49_249240


Mass: 16819.641 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JVC7

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Details

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: all / 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: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131707 / Symmetry type: POINT

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