ISDA: 9D5N

Deposition Date 2024-08-13

Release Date 2025-05-14

Last Version Date 2025-05-14

Entry Detail

PDB ID:

9D5N

Keywords:

STRUCTURAL PROTEIN

Title:

48-nm doublet microtubule from Trichomonas vaginalis strain G3

Biological Source:

Source Organism:

Trichomonas vaginalis G3 (Taxon ID: 412133)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

4.20 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Tubulin beta chain
Gene (Uniprot):TVAG_008680, TVAG_062880, TVAG_456920
Chain IDs:A (auth: 0), F (auth: Fl), G (auth: Fm), H (auth: Fn), I (auth: Fo), J (auth: Fp), K (auth: Fq), L (auth: Fr), M (auth: Fs), N (auth: A0), O (auth: Ft), P (auth: Fu), Q (auth: Fv), R (auth: Fw), S (auth: Fx), T (auth: Fy), U (auth: Fz), OA (auth: GH), BB (auth: GU), CB (auth: GV), DB (auth: GW), EB (auth: GX), FB (auth: GY), GB (auth: GZ), HB (auth: Ga), IB (auth: Gb), JB (auth: Gc), KB (auth: Gd), LB (auth: Ge), MB (auth: Gf), NB (auth: Gg), OB (auth: Gh), PB (auth: Gi), QB (auth: Gj), RB (auth: Gk), UB (auth: Gm), QC (auth: O), RC (auth: P), WC (auth: U), ZC (auth: X), AD (auth: A3), PD (auth: m), QD (auth: n), VD (auth: r), JE (auth: AA), KE (auth: AB), LE (auth: AC), ME (auth: AD), NE (auth: AE), OE (auth: AF), PE (auth: AG), QE (auth: AH), VE (auth: AL), WE (auth: AM), XE (auth: AN), YE (auth: AO), ZE (auth: AP), AF (auth: AQ), BF (auth: AR), CF (auth: AS), DF (auth: AT), EF (auth: AU), FF (auth: AV), GF (auth: AW), HF (auth: AX), IF (auth: AY), JF (auth: AZ), KF (auth: Aa), LF (auth: Ab), MF (auth: Ac), NF (auth: Ad), OF (auth: Ae), PF (auth: Af), QF (auth: Ag), RF (auth: Ah), SF (auth: Ai), WF (auth: Am), XF (auth: An), YF (auth: Ao), ZF (auth: Ap), AG (auth: Aq), BG (auth: Ar), CG (auth: As), DG (auth: At), EG (auth: Au), FG (auth: Av), KG (auth: Az), WG (auth: BA), XG (auth: BB), YG (auth: BC), ZG (auth: BD), AH (auth: BE), BH (auth: BF), CH (auth: BG), DH (auth: BH), TH (auth: BW), WH (auth: BZ), XH (auth: Ba), YH (auth: Bb), BI (auth: Be), CI (auth: Bf), DI (auth: Bg), EI (auth: Bh), FI (auth: Bi), GI (auth: Bj), HI (auth: Bk), II (auth: Bl), JI (auth: Bm), KI (auth: Bn), LI (auth: Bo), MI (auth: Bp), NI (auth: Bq), OI (auth: Br), PI (auth: Bs), QI (auth: Bt), DL, FL (auth: DM), GL (auth: DN), HL (auth: DO), IL (auth: DP), JL (auth: DQ), KL (auth: DR), LL (auth: DS), ML (auth: DT), NL (auth: DU), OL (auth: DV), PL (auth: DW), QL (auth: DX), RL (auth: DY), SL (auth: DZ), TL (auth: Da), UL (auth: Db), VL (auth: Dc), WL (auth: Dd), XL (auth: De), YL (auth: Df), ZL (auth: Dg), AM (auth: Dh), BM (auth: Di), CM (auth: Dj), DM (auth: Dk), EM (auth: Dq), FM (auth: Dr), GM (auth: Ds), HM (auth: Dt), IM (auth: Du), JM (auth: Dv), KM (auth: Dw), LM (auth: Dx), NM (auth: E0), XM (auth: E9), YM (auth: EL), ZM (auth: EM), AN (auth: EN), BN (auth: EO), CN (auth: EP), DN (auth: EQ), EN (auth: ER), FN (auth: ES), GN (auth: ET), HN (auth: EU), IN (auth: EV), JN (auth: EW), KN (auth: EX), LN (auth: EY), MN (auth: EZ), NN (auth: Ea), ON (auth: Eb), PN (auth: Ec), QN (auth: Ed), SN (auth: Ef), ZN (auth: 7), JO (auth: Ev), QO (auth: F1), RO (auth: F2), TO (auth: 8), UO (auth: F4), AP (auth: FA), BP (auth: FB), CP (auth: FC), DP (auth: FD), EP (auth: FE), FP (auth: FF), GP (auth: FG), HP (auth: FH), IP (auth: FI), JP (auth: FJ), KP (auth: FK), LP (auth: FL), NP (auth: FN), QP (auth: 9)
Chain Length:447
Number of Molecules:191
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2DC16 Pfam ID:PF03953, PF00091

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:FAP21
Gene (Uniprot):TVAG_222530
Chain IDs:B (auth: A)
Chain Length:452
Number of Molecules:1
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2F5C9

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Trichohyalin-plectin-homology domain-containing protein
Gene (Uniprot):TVAG_239860
Chain IDs:LG (auth: B), YI (auth: C)
Chain Length:452
Number of Molecules:2
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2EFC9

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Parkin co-regulated protein
Gene (Uniprot):TVAG_377800
Chain IDs:AJ (auth: C2), BJ (auth: C3), BL (auth: Cz)
Chain Length:236
Number of Molecules:3
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2DAX1 Pfam ID:PF10274

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Enkurin
Gene (Uniprot):TVAG_061940
Chain IDs:EJ (auth: CC), AK (auth: CY), BK (auth: CZ), OO (auth: F)
Chain Length:241
Number of Molecules:4
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2E7V9 Pfam ID:PF13864

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:FAP77
Gene (Uniprot):TVAG_323650
Chain IDs:HJ (auth: CF), EK (auth: Cc), HK (auth: Cf), IK (auth: Cg)
Chain Length:241
Number of Molecules:4
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2FTW1 Pfam ID:PF14825

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:EF hand family protein
Gene (Uniprot):TVAG_527160
Chain IDs:IJ (auth: CG), JK (auth: Ch), KK (auth: Ci), LK (auth: Cj), MK (auth: Ck), NK (auth: Cl), MM (auth: E)
Chain Length:918
Number of Molecules:7
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2G843

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 52
Gene (Uniprot):TVAG_030160
Chain IDs:JJ (auth: CH), FK (auth: Cd), GK (auth: Ce), CL (auth: D)
Chain Length:605
Number of Molecules:4
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2FVE3 Pfam ID:PF00400

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleoside diphosphate kinase
Gene (Uniprot):TVAG_498410
Chain IDs:OJ (auth: CM), QJ (auth: CO), RJ (auth: CP)
Chain Length:375
Number of Molecules:3
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2E829 Pfam ID:PF00334

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:FAP161
Gene (Uniprot):TVAG_194820
Chain IDs:PJ (auth: CN), SJ (auth: CQ)
Chain Length:249
Number of Molecules:2
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2FL25

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIIa domain-containing protein
Gene (Uniprot):TVAG_208920
Chain IDs:TJ (auth: CR)
Chain Length:75
Number of Molecules:1
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2DVD4

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:FAP12
Gene (Uniprot):TVAG_395370
Chain IDs:UJ (auth: CS)
Chain Length:108
Number of Molecules:1
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2F1C6 Pfam ID:PF15104

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Meiosis-specific nuclear structural protein 1
Gene (Uniprot):TVAG_123230
Chain IDs:VJ (auth: CT), WJ (auth: CU)
Chain Length:595
Number of Molecules:2
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2FH94 Pfam ID:PF13868

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:MGC84469 protein, putative
Gene (Uniprot):TVAG_159140
Chain IDs:YJ (auth: CW), QK (auth: Co), RK (auth: Cp), SK (auth: Cq), TK (auth: Cr), UK (auth: Cs), VK (auth: Ct)
Chain Length:375
Number of Molecules:7
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2GCC1 Pfam ID:PF06565

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Tubulin alpha chain
Gene (Uniprot):TVAG_196270, TVAG_206890, TVAG_312330, TVAG_359090, TVAG_360870
Chain IDs:C (auth: Fi), D (auth: Fj), E (auth: Fk), X (auth: G1), Y (auth: G2), Z (auth: G3), AA (auth: G4), BA (auth: G5), CA (auth: G6), GA, HA (auth: GB), IA (auth: GC), JA (auth: GD), KA (auth: GE), LA (auth: A1), MA (auth: GF), NA (auth: GG), PA (auth: GI), QA (auth: GJ), RA (auth: GK), SA (auth: GL), TA (auth: GM), UA (auth: GN), VA (auth: GO), WA (auth: GP), XA (auth: GQ), YA (auth: GR), ZA (auth: GS), AB (auth: GT), SB (auth: A2), TB (auth: Gl), VB (auth: Gn), WB (auth: Go), XB (auth: Gp), YB (auth: Gq), ZB (auth: Gr), AC (auth: Gs), BC (auth: Gt), CC (auth: Gu), DC (auth: Gv), EC (auth: Gw), FC (auth: Gx), GC (auth: Gy), HC (auth: Gz), SC (auth: Q), TC (auth: R), UC (auth: S), VC (auth: T), XC (auth: V), YC (auth: W), BD (auth: Y), CD (auth: Z), DD (auth: a), ED (auth: b), FD (auth: c), GD (auth: d), HD (auth: e), ID (auth: f), JD (auth: g), KD (auth: h), LD (auth: i), MD (auth: j), ND (auth: k), OD (auth: l), RD (auth: o), SD (auth: p), TD (auth: A4), UD (auth: q), WD (auth: s), XD (auth: t), YD (auth: u), ZD (auth: v), AE (auth: w), BE (auth: x), CE (auth: y), DE (auth: z), EE (auth: A5), FE (auth: A6), GE (auth: A7), HE (auth: A8), IE (auth: A9), RE (auth: AI), SE (auth: AJ), TE (auth: AK), UE (auth: 1), TF (auth: Aj), UF (auth: Ak), VF (auth: Al), GG (auth: 2), HG (auth: Aw), IG (auth: Ax), JG (auth: Ay), MG (auth: B0), NG (auth: B1), OG (auth: B2), PG (auth: B3), QG (auth: B4), RG (auth: B5), SG (auth: B6), TG (auth: B7), UG (auth: B8), VG (auth: B9), EH (auth: BI), FH (auth: BJ), GH (auth: BK), HH (auth: BL), IH (auth: BM), JH (auth: BN), KH (auth: BO), LH (auth: 3), MH (auth: BP), NH (auth: BQ), OH (auth: BR), PH (auth: BS), QH (auth: BT), RH (auth: BU), SH (auth: BV), UH (auth: BX), VH (auth: BY), ZH (auth: Bc), AI (auth: Bd), RI (auth: Bu), SI (auth: 4), TI (auth: Bv), UI (auth: Bw), VI (auth: Bx), WI (auth: By), XI (auth: Bz), CJ (auth: CA), DJ (auth: CB), EL (auth: 5), OM (auth: E1), PM (auth: E2), QM (auth: E3), RM (auth: 6), SM (auth: E4), TM (auth: E5), UM (auth: E6), VM (auth: E7), WM (auth: E8), RN (auth: Ee), TN (auth: Eg), UN (auth: Eh), VN (auth: Ei), WN (auth: Ej), XN (auth: Ek), YN (auth: El), AO (auth: Em), BO (auth: En), CO (auth: Eo), DO (auth: Ep), EO (auth: Eq), FO (auth: Er), GO (auth: Es), HO (auth: Et), IO (auth: Eu), KO (auth: Ew), LO (auth: Ex), MO (auth: Ey), NO (auth: Ez), PO (auth: F0), SO (auth: F3), VO (auth: F5), WO (auth: F6), XO (auth: F7), YO (auth: F8), ZO (auth: F9), MP (auth: FM), OP (auth: FO), PP (auth: FP), RP (auth: FQ), SP (auth: FR), TP (auth: FS), UP (auth: FT), VP (auth: FU), WP (auth: FV), XP (auth: FW), YP (auth: FX), ZP (auth: FY), AQ (auth: FZ), BQ (auth: Fa), CQ (auth: Fb), DQ (auth: Fc), EQ (auth: Fd), FQ (auth: Fe), GQ (auth: Ff), HQ (auth: Fg), IQ (auth: Fh)
Chain Length:452
Number of Molecules:188
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2E8B1 Pfam ID:PF03953, PF00091

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:IQ calmodulin-binding motif family protein
Gene (Uniprot):TVAG_165330
Chain IDs:V (auth: G), FJ (auth: CD), CK (auth: Ca), DK (auth: Cb)
Chain Length:306
Number of Molecules:4
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2DUL4

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Flagellar protofilament ribbon protein, putative
Gene (Uniprot):TVAG_352320
Chain IDs:W (auth: G0), DA (auth: G7), EA (auth: G8), FA (auth: G9)
Chain Length:383
Number of Molecules:4
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2FZ95 Pfam ID:PF05914

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:TvFAP40
Gene (Uniprot):TVAG_347810
Chain IDs:IC (auth: H), GJ (auth: CE), OK (auth: Cm), PK (auth: Cn)
Chain Length:377
Number of Molecules:4
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2DSS2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Parkin co-regulated protein
Gene (Uniprot):TVAG_342930
Chain IDs:JC (auth: HA), KC (auth: HB), LC (auth: HC), MC (auth: HD)
Chain Length:241
Number of Molecules:4
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2EJQ5 Pfam ID:PF10274

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 45
Gene (Uniprot):TVAG_314720
Chain IDs:NC (auth: I), LJ (auth: CJ), MJ (auth: CK), NJ (auth: CL)
Chain Length:465
Number of Molecules:4
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2ETR1 Pfam ID:PF13868

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 20
Gene (Uniprot):TVAG_109520, TVAG_450050
Chain IDs:OC (auth: M), ZI (auth: C1), KJ (auth: CI), WK (auth: Cu), XK (auth: Cv), YK (auth: Cw), ZK (auth: Cx), AL (auth: Cy)
Chain Length:192
Number of Molecules:8
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2EAE1 Pfam ID:PF05018

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 53
Gene (Uniprot):TVAG_436250
Chain IDs:PC (auth: N), XJ (auth: CV), ZJ (auth: CX)
Chain Length:192
Number of Molecules:3
Biological Source:Trichomonas vaginalis G3

UniProt ID:A2G223 Pfam ID:PF13868

Ligand Molecules

GDP

GTP

Primary Citation

Structures of Native Doublet Microtubules from Trichomonas vaginalis Reveal Parasite-Specific Proteins.

Stevens, A, Kashyap, S, Crofut, E.H, Wang, S.E, Muratore, K.A, Johnson, P.J, Zhou, Z.H.Show

Nat Commun 16 3996 3996 (2025)

PMID: 40301421 DOI: 10.1038/s41467-025-59369-y

Abstact

Doublet microtubules (DMTs) are flagellar components required for the protist Trichomonas vaginalis (Tv) to swim through the human genitourinary tract to cause trichomoniasis, the most common non-viral sexually transmitted disease. Lack of structures of Tv's DMT (Tv-DMT) has prevented structure-guided drug design to manage Tv infection. Here, we determine the 16 nm, 32 nm, 48 nm and 96 nm-repeat structures of native Tv-DMT at resolution ranging from 3.4 to 4.4 Å by cryogenic electron microscopy (cryoEM) and built an atomic model for the entire Tv-DMT. These structures show that Tv-DMT is composed of 30 different proteins, including the α- and β-tubulin, 19 microtubule inner proteins (MIPs) and 9 microtubule outer proteins. While the A-tubule of Tv-DMT is simplistic compared to DMTs of other organisms, the B-tubule of Tv-DMT features parasite-specific proteins, such as TvFAP40 and TvFAP35. Notably, TvFAP40 and TvFAP35 form filaments near the inner and outer junctions, respectively, and interface with stabilizing MIPs. This atomic model of the Tv-DMT highlights diversity of eukaryotic motility machineries and provides a structural framework to inform rational design of therapeutics against trichomoniasis.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

Feedback Form