9YA1 | pdb_00009ya1

Cryo-EM structure of intraconoidal microtubule 2 (ICMT2) from Toxoplasma gondii (8-nm repeat)

PDB DOI: https://doi.org/10.2210/pdb9YA1/pdb
EM Map EMD-72717: EMDB EMDataResource

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: 3.52 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Atomic models of the Toxoplasma cell invasion machinery

Zeng, J., Fu, Y., Qian, P., 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

Macromolecule Content

Total Structure Weight: 4,458.06 kDa
Atom Count: 226,608
Modeled Residue Count: 28,687
Deposited Residue Count: 39,706
Unique protein chains: 8

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ICMAP4, TGME49_225340	A [auth 1], B [auth 2]	2,041	Toxoplasma gondii	Mutation(s): 0
UniProt
Find proteins for A0A086KM91 (Toxoplasma gondii GAB2-2007-GAL-DOM2) Explore A0A086KM91 Go to UniProtKB: A0A086KM91
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A086KM91
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Microtubule associated protein SPM1	C [auth A] FB [auth F] IB [auth G] JA [auth D] JB [auth H] C [auth A], FB [auth F], IB [auth G], JA [auth D], JB [auth H], KB [auth I], LB [auth J], MB [auth K], N [auth B], UA [auth E], Y [auth C]	351	Toxoplasma gondii	Mutation(s): 0
UniProt
Find proteins for A0A7J6K285 (Toxoplasma gondii) Explore A0A7J6K285 Go to UniProtKB: A0A7J6K285
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7J6K285
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	BA [auth C2] BB [auth E6] D [auth A0] DA [auth C4] DB [auth E8] BA [auth C2], BB [auth E6], D [auth A0], DA [auth C4], DB [auth E8], F [auth A2], FA [auth C6], GB [auth F0], H [auth A4], HA [auth C8], J [auth A6], KA [auth D0], L [auth A8], MA [auth D2], O [auth B0], OA [auth D4], Q [auth B2], QA [auth D6], S [auth B4], SA [auth D8], U [auth B6], VA [auth E0], W [auth B8], XA [auth E2], Z [auth C0], ZA [auth E4]	453	Toxoplasma gondii	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P10873 (Toxoplasma gondii) Explore P10873 Go to UniProtKB: P10873
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10873
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	AA [auth C1] AB [auth E5] CA [auth C3] CB [auth E7] E [auth A1] AA [auth C1], AB [auth E5], CA [auth C3], CB [auth E7], E [auth A1], EA [auth C5], EB [auth E9], G [auth A3], GA [auth C7], HB [auth F1], I [auth A5], IA [auth C9], K [auth A7], LA [auth D1], M [auth A9], NA [auth D3], P [auth B1], PA [auth D5], R [auth B3], RA [auth D7], T [auth B5], TA [auth D9], V [auth B7], WA [auth E1], X [auth B9], YA [auth E3]	449	Toxoplasma gondii	Mutation(s): 0
UniProt
Find proteins for I7BFC9 (Toxoplasma gondii) Explore I7BFC9 Go to UniProtKB: I7BFC9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7BFC9
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
TLAP3 (apical cap protein AC5), TGME49_235380	NB [auth O], OB [auth P], PB [auth R]	583	Toxoplasma gondii	Mutation(s): 0
UniProt
Find proteins for A0A151H4L4 (Toxoplasma gondii TgCatPRC2) Explore A0A151H4L4 Go to UniProtKB: A0A151H4L4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A151H4L4
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
TLAP4 (thioredoxin-like associated protein), TGME49_201760	QB [auth U], RB [auth V], SB [auth W], TB [auth X]	336	Toxoplasma gondii	Mutation(s): 0
UniProt
Find proteins for A0A7J6K913 (Toxoplasma gondii) Explore A0A7J6K913 Go to UniProtKB: A0A7J6K913
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7J6K913
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
TRXL1, TGME49_232410	AC [auth g] BC [auth h] CC [auth i] DC [auth j] GC [auth m] AC [auth g], BC [auth h], CC [auth i], DC [auth j], GC [auth m], HC [auth n], IC [auth o], JC [auth p], KC [auth q], LC [auth r], MC [auth s], NC [auth t], OC [auth u], PC [auth v], QC [auth w], RC [auth x], UB [auth a], VB [auth b], WB [auth c], XB [auth d], YB [auth e], ZB [auth f]	220	Toxoplasma gondii	Mutation(s): 0
UniProt
Find proteins for Q8MPF4 (Toxoplasma gondii) Explore Q8MPF4 Go to UniProtKB: Q8MPF4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8MPF4
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
TRXL2, TGME49_225790	EC [auth k], FC [auth l]	189	Toxoplasma gondii	Mutation(s): 0
UniProt
Find proteins for A0A7J6K232 (Toxoplasma gondii) Explore A0A7J6K232 Go to UniProtKB: A0A7J6K232
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7J6K232
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain AE [auth C4] SDF format, chain BD [auth A6] SDF format, chain DE [auth C6] SDF format, chain ED [auth A8] SDF format, chain EF [auth E4] SDF format, chain GD [auth B0] SDF format, chain ID [auth B2] SDF format, chain IF [auth E7] SDF format, chain JE [auth D0] SDF format, chain KF [auth E8] SDF format, chain LD [auth B4] SDF format, chain ME [auth D2] SDF format, chain NF [auth F0] SDF format, chain OD [auth B6] SDF format, chain PE [auth D4] SDF format, chain SD [auth B8] SDF format, chain SE [auth D6] SDF format, chain UD [auth C0] SDF format, chain VE [auth D8] SDF format, chain WC [auth A2] SDF format, chain XD [auth C2] SDF format, chain YC [auth A4] SDF format, chain YE [auth E0] SDF format, chain SC [auth A0] SDF format, chain GE [auth C8] SDF format, chain BF [auth E2] MOL2 format, chain AE [auth C4] MOL2 format, chain BD [auth A6] MOL2 format, chain DE [auth C6] MOL2 format, chain ED [auth A8] MOL2 format, chain EF [auth E4] MOL2 format, chain GD [auth B0] MOL2 format, chain ID [auth B2] MOL2 format, chain IF [auth E7] MOL2 format, chain JE [auth D0] MOL2 format, chain KF [auth E8] MOL2 format, chain LD [auth B4] MOL2 format, chain ME [auth D2] MOL2 format, chain NF [auth F0] MOL2 format, chain OD [auth B6] MOL2 format, chain PE [auth D4] MOL2 format, chain SD [auth B8] MOL2 format, chain SE [auth D6] MOL2 format, chain UD [auth C0] MOL2 format, chain VE [auth D8] MOL2 format, chain WC [auth A2] MOL2 format, chain XD [auth C2] MOL2 format, chain YC [auth A4] MOL2 format, chain YE [auth E0] MOL2 format, chain SC [auth A0] MOL2 format, chain GE [auth C8] MOL2 format, chain BF [auth E2] mmCIF format, chain AE [auth C4] mmCIF format, chain BD [auth A6] mmCIF format, chain DE [auth C6] mmCIF format, chain ED [auth A8] mmCIF format, chain EF [auth E4] mmCIF format, chain GD [auth B0] mmCIF format, chain ID [auth B2] mmCIF format, chain IF [auth E7] mmCIF format, chain JE [auth D0] mmCIF format, chain KF [auth E8] mmCIF format, chain LD [auth B4] mmCIF format, chain ME [auth D2] mmCIF format, chain NF [auth F0] mmCIF format, chain OD [auth B6] mmCIF format, chain PE [auth D4] mmCIF format, chain SD [auth B8] mmCIF format, chain SE [auth D6] mmCIF format, chain UD [auth C0] mmCIF format, chain VE [auth D8] mmCIF format, chain WC [auth A2] mmCIF format, chain XD [auth C2] mmCIF format, chain YC [auth A4] mmCIF format, chain YE [auth E0] mmCIF format, chain SC [auth A0] mmCIF format, chain GE [auth C8] mmCIF format, chain BF [auth E2]	AE [auth C4] BD [auth A6] BF [auth E2] DE [auth C6] ED [auth A8] AE [auth C4], BD [auth A6], BF [auth E2], DE [auth C6], ED [auth A8], EF [auth E4], GD [auth B0], GE [auth C8], ID [auth B2], IF [auth E7], JE [auth D0], KF [auth E8], LD [auth B4], ME [auth D2], NF [auth F0], OD [auth B6], PE [auth D4], SC [auth A0], SD [auth B8], SE [auth D6], UD [auth C0], VE [auth D8], WC [auth A2], XD [auth C2], YC [auth A4], YE [auth E0]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain AE [auth C4] Focus chain BD [auth A6] Focus chain BF [auth E2] Focus chain DE [auth C6] Focus chain ED [auth A8] Focus chain EF [auth E4] Focus chain GD [auth B0] Focus chain GE [auth C8] Focus chain ID [auth B2] Focus chain IF [auth E7] Focus chain JE [auth D0] Focus chain KF [auth E8] Focus chain LD [auth B4] Focus chain ME [auth D2] Focus chain NF [auth F0] Focus chain OD [auth B6] Focus chain PE [auth D4] Focus chain SC [auth A0] Focus chain SD [auth B8] Focus chain SE [auth D6] Focus chain UD [auth C0] Focus chain VE [auth D8] Focus chain WC [auth A2] Focus chain XD [auth C2] Focus chain YC [auth A4] Focus chain YE [auth E0] Interactions & Density Focus chain AE [auth C4] Focus chain BD [auth A6] Focus chain BF [auth E2] Focus chain DE [auth C6] Focus chain ED [auth A8] Focus chain EF [auth E4] Focus chain GD [auth B0] Focus chain GE [auth C8] Focus chain ID [auth B2] Focus chain IF [auth E7] Focus chain JE [auth D0] Focus chain KF [auth E8] Focus chain LD [auth B4] Focus chain ME [auth D2] Focus chain NF [auth F0] Focus chain OD [auth B6] Focus chain PE [auth D4] Focus chain SC [auth A0] Focus chain SD [auth B8] Focus chain SE [auth D6] Focus chain UD [auth C0] Focus chain VE [auth D8] Focus chain WC [auth A2] Focus chain XD [auth C2] Focus chain YC [auth A4] Focus chain YE [auth E0]
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain AD [auth A5] SDF format, chain AF [auth E1] SDF format, chain DD [auth A7] SDF format, chain DF [auth E3] SDF format, chain FE [auth C7] SDF format, chain GF [auth E5] SDF format, chain IE [auth C9] SDF format, chain KD [auth B3] SDF format, chain LE [auth D1] SDF format, chain MF [auth E9] SDF format, chain ND [auth B5] SDF format, chain OE [auth D3] SDF format, chain QD [auth B7] SDF format, chain QF [auth O] SDF format, chain RE [auth D5] SDF format, chain RF [auth P] SDF format, chain UC [auth A1] SDF format, chain UE [auth D7] SDF format, chain WD [auth C1] SDF format, chain XC [auth A3] SDF format, chain XE [auth D9] SDF format, chain ZD [auth C3] SDF format, chain TD [auth B9] SDF format, chain PF [auth F1] SDF format, chain JF [auth E7] SDF format, chain CE [auth C5] MOL2 format, chain AD [auth A5] MOL2 format, chain AF [auth E1] MOL2 format, chain DD [auth A7] MOL2 format, chain DF [auth E3] MOL2 format, chain FE [auth C7] MOL2 format, chain GF [auth E5] MOL2 format, chain IE [auth C9] MOL2 format, chain KD [auth B3] MOL2 format, chain LE [auth D1] MOL2 format, chain MF [auth E9] MOL2 format, chain ND [auth B5] MOL2 format, chain OE [auth D3] MOL2 format, chain QD [auth B7] MOL2 format, chain QF [auth O] MOL2 format, chain RE [auth D5] MOL2 format, chain RF [auth P] MOL2 format, chain UC [auth A1] MOL2 format, chain UE [auth D7] MOL2 format, chain WD [auth C1] MOL2 format, chain XC [auth A3] MOL2 format, chain XE [auth D9] MOL2 format, chain ZD [auth C3] MOL2 format, chain TD [auth B9] MOL2 format, chain PF [auth F1] MOL2 format, chain JF [auth E7] MOL2 format, chain CE [auth C5] mmCIF format, chain AD [auth A5] mmCIF format, chain AF [auth E1] mmCIF format, chain DD [auth A7] mmCIF format, chain DF [auth E3] mmCIF format, chain FE [auth C7] mmCIF format, chain GF [auth E5] mmCIF format, chain IE [auth C9] mmCIF format, chain KD [auth B3] mmCIF format, chain LE [auth D1] mmCIF format, chain MF [auth E9] mmCIF format, chain ND [auth B5] mmCIF format, chain OE [auth D3] mmCIF format, chain QD [auth B7] mmCIF format, chain QF [auth O] mmCIF format, chain RE [auth D5] mmCIF format, chain RF [auth P] mmCIF format, chain UC [auth A1] mmCIF format, chain UE [auth D7] mmCIF format, chain WD [auth C1] mmCIF format, chain XC [auth A3] mmCIF format, chain XE [auth D9] mmCIF format, chain ZD [auth C3] mmCIF format, chain TD [auth B9] mmCIF format, chain PF [auth F1] mmCIF format, chain JF [auth E7] mmCIF format, chain CE [auth C5]	AD [auth A5] AF [auth E1] CE [auth C5] DD [auth A7] DF [auth E3] AD [auth A5], AF [auth E1], CE [auth C5], DD [auth A7], DF [auth E3], FE [auth C7], GF [auth E5], IE [auth C9], JF [auth E7], KD [auth B3], LE [auth D1], MF [auth E9], ND [auth B5], OE [auth D3], PF [auth F1], QD [auth B7], QF [auth O], RE [auth D5], RF [auth P], TD [auth B9], UC [auth A1], UE [auth D7], WD [auth C1], XC [auth A3], XE [auth D9], ZD [auth C3]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain AD [auth A5] Focus chain AF [auth E1] Focus chain CE [auth C5] Focus chain DD [auth A7] Focus chain DF [auth E3] Focus chain FE [auth C7] Focus chain GF [auth E5] Focus chain IE [auth C9] Focus chain JF [auth E7] Focus chain KD [auth B3] Focus chain LE [auth D1] Focus chain MF [auth E9] Focus chain ND [auth B5] Focus chain OE [auth D3] Focus chain PF [auth F1] Focus chain QD [auth B7] Focus chain QF [auth O] Focus chain RE [auth D5] Focus chain RF [auth P] Focus chain TD [auth B9] Focus chain UC [auth A1] Focus chain UE [auth D7] Focus chain WD [auth C1] Focus chain XC [auth A3] Focus chain XE [auth D9] Focus chain ZD [auth C3] Interactions & Density Focus chain AD [auth A5] Focus chain AF [auth E1] Focus chain CE [auth C5] Focus chain DD [auth A7] Focus chain DF [auth E3] Focus chain FE [auth C7] Focus chain GF [auth E5] Focus chain IE [auth C9] Focus chain JF [auth E7] Focus chain KD [auth B3] Focus chain LE [auth D1] Focus chain MF [auth E9] Focus chain ND [auth B5] Focus chain OE [auth D3] Focus chain PF [auth F1] Focus chain QD [auth B7] Focus chain QF [auth O] Focus chain RE [auth D5] Focus chain RF [auth P] Focus chain TD [auth B9] Focus chain UC [auth A1] Focus chain UE [auth D7] Focus chain WD [auth C1] Focus chain XC [auth A3] Focus chain XE [auth D9] Focus chain ZD [auth C3]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BE [auth C4] SDF format, chain CD [auth A6] SDF format, chain CF [auth E2] SDF format, chain EE [auth C6] SDF format, chain FF [auth E4] SDF format, chain HD [auth B0] SDF format, chain HE [auth C9] SDF format, chain HF [auth E6] SDF format, chain JD [auth B2] SDF format, chain KE [auth D1] SDF format, chain MD [auth B4] SDF format, chain OF [auth F0] SDF format, chain QE [auth D4] SDF format, chain RD [auth B8] SDF format, chain TC [auth A0] SDF format, chain TE [auth D6] SDF format, chain VC [auth A2] SDF format, chain VD [auth C0] SDF format, chain YD [auth C2] SDF format, chain ZC [auth A4] SDF format, chain ZE [auth E0] SDF format, chain WE [auth D8] SDF format, chain PD [auth B6] SDF format, chain NE [auth D3] SDF format, chain LF [auth E8] SDF format, chain FD [auth A8] MOL2 format, chain BE [auth C4] MOL2 format, chain CD [auth A6] MOL2 format, chain CF [auth E2] MOL2 format, chain EE [auth C6] MOL2 format, chain FF [auth E4] MOL2 format, chain HD [auth B0] MOL2 format, chain HE [auth C9] MOL2 format, chain HF [auth E6] MOL2 format, chain JD [auth B2] MOL2 format, chain KE [auth D1] MOL2 format, chain MD [auth B4] MOL2 format, chain OF [auth F0] MOL2 format, chain QE [auth D4] MOL2 format, chain RD [auth B8] MOL2 format, chain TC [auth A0] MOL2 format, chain TE [auth D6] MOL2 format, chain VC [auth A2] MOL2 format, chain VD [auth C0] MOL2 format, chain YD [auth C2] MOL2 format, chain ZC [auth A4] MOL2 format, chain ZE [auth E0] MOL2 format, chain WE [auth D8] MOL2 format, chain PD [auth B6] MOL2 format, chain NE [auth D3] MOL2 format, chain LF [auth E8] MOL2 format, chain FD [auth A8] mmCIF format, chain BE [auth C4] mmCIF format, chain CD [auth A6] mmCIF format, chain CF [auth E2] mmCIF format, chain EE [auth C6] mmCIF format, chain FF [auth E4] mmCIF format, chain HD [auth B0] mmCIF format, chain HE [auth C9] mmCIF format, chain HF [auth E6] mmCIF format, chain JD [auth B2] mmCIF format, chain KE [auth D1] mmCIF format, chain MD [auth B4] mmCIF format, chain OF [auth F0] mmCIF format, chain QE [auth D4] mmCIF format, chain RD [auth B8] mmCIF format, chain TC [auth A0] mmCIF format, chain TE [auth D6] mmCIF format, chain VC [auth A2] mmCIF format, chain VD [auth C0] mmCIF format, chain YD [auth C2] mmCIF format, chain ZC [auth A4] mmCIF format, chain ZE [auth E0] mmCIF format, chain WE [auth D8] mmCIF format, chain PD [auth B6] mmCIF format, chain NE [auth D3] mmCIF format, chain LF [auth E8] mmCIF format, chain FD [auth A8]	BE [auth C4] CD [auth A6] CF [auth E2] EE [auth C6] FD [auth A8] BE [auth C4], CD [auth A6], CF [auth E2], EE [auth C6], FD [auth A8], FF [auth E4], HD [auth B0], HE [auth C9], HF [auth E6], JD [auth B2], KE [auth D1], LF [auth E8], MD [auth B4], NE [auth D3], OF [auth F0], PD [auth B6], QE [auth D4], RD [auth B8], TC [auth A0], TE [auth D6], VC [auth A2], VD [auth C0], WE [auth D8], YD [auth C2], ZC [auth A4], ZE [auth E0]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BE [auth C4] Focus chain CD [auth A6] Focus chain CF [auth E2] Focus chain EE [auth C6] Focus chain FD [auth A8] Focus chain FF [auth E4] Focus chain HD [auth B0] Focus chain HE [auth C9] Focus chain HF [auth E6] Focus chain JD [auth B2] Focus chain KE [auth D1] Focus chain LF [auth E8] Focus chain MD [auth B4] Focus chain NE [auth D3] Focus chain OF [auth F0] Focus chain PD [auth B6] Focus chain QE [auth D4] Focus chain RD [auth B8] Focus chain TC [auth A0] Focus chain TE [auth D6] Focus chain VC [auth A2] Focus chain VD [auth C0] Focus chain WE [auth D8] Focus chain YD [auth C2] Focus chain ZC [auth A4] Focus chain ZE [auth E0] Interactions & Density Focus chain BE [auth C4] Focus chain CD [auth A6] Focus chain CF [auth E2] Focus chain EE [auth C6] Focus chain FD [auth A8] Focus chain FF [auth E4] Focus chain HD [auth B0] Focus chain HE [auth C9] Focus chain HF [auth E6] Focus chain JD [auth B2] Focus chain KE [auth D1] Focus chain LF [auth E8] Focus chain MD [auth B4] Focus chain NE [auth D3] Focus chain OF [auth F0] Focus chain PD [auth B6] Focus chain QE [auth D4] Focus chain RD [auth B8] Focus chain TC [auth A0] Focus chain TE [auth D6] Focus chain VC [auth A2] Focus chain VD [auth C0] Focus chain WE [auth D8] Focus chain YD [auth C2] Focus chain ZC [auth A4] Focus chain ZE [auth E0]