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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 / cytoplasm / cytosol
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 / Filamin/ABP280 repeat / Tetratricopeptide repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Ca2+ insensitive EF hand / 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 / Cyclic nucleotide-binding domain signature 2. / 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 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. / von Willebrand factor A-like domain superfamily / Pleckstrin homology domain. / 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: To Be Published
Title: Atomic models of the conoid, the cell invasion machinery of the human parasite Toxoplasma gondii
Authors: Zeng, J. / Fu, Y. / Qian, P. / Sibley, L.D. / Zhang, R.
History
DepositionSep 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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