9YA2 | pdb_00009ya2

Cryo-EM structure of intraconoidal microtubule 1 (ICMT1) from Toxoplasma gondii (8-nm repeat)

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Toxoplasma gondii
  • Mutation(s): No 

  • Deposited: 2025-09-15 Released: 2025-12-03 
  • Deposition Author(s): Zeng, J., Zhang, R.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic models of the Toxoplasma cell invasion machinery.

Zeng, J.Fu, Y.Qian, P.Huang, W.Niu, Q.Beatty, W.L.Brown, A.Sibley, L.D.Zhang, R.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-025-01728-w
  • Primary Citation of Related Structures:  
    9Y9Z, 9YA0, 9YA1, 9YA2, 9YA3

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microtubule associated protein SPM1351Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K285 (Toxoplasma gondii)
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UniProt GroupA0A7J6K285
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha chain453Toxoplasma gondiiMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P10873 (Toxoplasma gondii)
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UniProt GroupP10873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain449Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for I7BFC9 (Toxoplasma gondii)
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UniProt GroupI7BFC9
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ICMAP2, TGME49_2247001,678Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A086KMN2 (Toxoplasma gondii GAB2-2007-GAL-DOM2)
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UniProt GroupA0A086KMN2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TLAP3 (apical cap protein AC5), TGME49_235380OB [auth O],
PB [auth P]
583Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A151H4L4 (Toxoplasma gondii TgCatPRC2)
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UniProt GroupA0A151H4L4
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
TLAP4 (thioredoxin-like associated protein), TGME49_201760RB [auth R],
SB [auth S],
TB [auth T],
UB [auth U]
336Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K913 (Toxoplasma gondii)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
TRXL1, TGME49_232410220Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for Q8MPF4 (Toxoplasma gondii)
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UniProt GroupQ8MPF4
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
TRXL2, TGME49_225790HC [auth k],
IC [auth l]
189Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K232 (Toxoplasma gondii)
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UniProt GroupA0A7J6K232
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

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AF [auth D8]
BD [auth A4]
DE [auth C3]
DF [auth E0]
ED [auth A6]
AF [auth D8],
BD [auth A4],
DE [auth C3],
DF [auth E0],
ED [auth A6],
FE [auth C4],
GF [auth E2],
HD [auth A8],
IE [auth C6],
JF [auth E4],
KD [auth B0],
LE [auth C8],
MF [auth E6],
ND [auth B2],
OE [auth D0],
PF [auth E8],
QD [auth B4],
RE [auth D2],
SF [auth F0],
TD [auth B6],
UE [auth D4],
VC [auth A0],
WD [auth B8],
XE [auth D6],
YC [auth A2],
ZD [auth C0]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
AD [auth A3]
BE [auth C1]
CF [auth D9]
DD [auth A5]
EE [auth C3]
AD [auth A3],
BE [auth C1],
CF [auth D9],
DD [auth A5],
EE [auth C3],
FF [auth E1],
GD [auth A7],
HE [auth C5],
IF [auth E3],
JD [auth A9],
KE [auth C7],
LF [auth E5],
MD [auth B1],
NE [auth C9],
OF [auth E7],
PD [auth B3],
QE [auth D1],
RF [auth E9],
SD [auth B5],
TE [auth D3],
UF [auth F1],
VD [auth B7],
WE [auth D5],
XC [auth A1],
YD [auth B9],
ZE [auth D7]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AE [auth C0]
BF [auth D8]
CD [auth A5]
CE [auth C2]
EF [auth E1]
AE [auth C0],
BF [auth D8],
CD [auth A5],
CE [auth C2],
EF [auth E1],
FD [auth A7],
GE [auth C4],
HF [auth E2],
ID [auth A8],
JE [auth C6],
KF [auth E4],
LD [auth B0],
ME [auth C8],
NF [auth E6],
OD [auth B2],
PE [auth D0],
QF [auth E9],
RD [auth B4],
SE [auth D2],
TF [auth F0],
UD [auth B6],
VE [auth D4],
WC [auth A0],
XD [auth B8],
YE [auth D6],
ZC [auth A2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI179885

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references
  • Version 1.2: 2025-12-24
    Changes: Data collection, Database references