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- PDB-9d5n: 48-nm doublet microtubule from Trichomonas vaginalis strain G3 -

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Basic information

Entry
Database: PDB / ID: 9d5n
Title48-nm doublet microtubule from Trichomonas vaginalis strain G3
Components
  • (Cilia- and flagella-associated protein ...) x 4
  • (Parkin co-regulated ...) x 2
  • EF hand family protein
  • Enkurin
  • FAP12
  • FAP161
  • FAP21
  • FAP77
  • Flagellar protofilament ribbon protein, putative
  • IQ calmodulin-binding motif family protein
  • MGC84469 protein, putative
  • Meiosis-specific nuclear structural protein 1
  • Nucleoside diphosphate kinase
  • RIIa domain-containing protein
  • Trichohyalin-plectin-homology domain-containing protein
  • Tubulin alpha chain
  • Tubulin beta chain
  • TvFAP40
KeywordsSTRUCTURAL PROTEIN / doublet microtubule / tubulin / flagella
Function / homology
Function and homology information


cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / axonemal microtubule / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / positive regulation of cell motility / nucleoside diphosphate kinase activity / motile cilium / GTP biosynthetic process ...cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / axonemal microtubule / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / positive regulation of cell motility / nucleoside diphosphate kinase activity / motile cilium / GTP biosynthetic process / mitotic cytokinesis / axoneme / cilium assembly / alpha-tubulin binding / Hsp70 protein binding / mitotic spindle organization / meiotic cell cycle / Hsp90 protein binding / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic spindle / mitotic cell cycle / microtubule / cytoskeleton / calmodulin binding / hydrolase activity / cilium / ciliary basal body / GTPase activity / GTP binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / Echinoderm microtubule-associated protein first beta-propeller / Cilia- and flagella-associated protein 77 / Cilia- and flagella-associated protein 77 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 141 / : / : / Meiosis-specific nuclear structural protein 1 / Cilia- and flagella-associated protein 45 ...: / Echinoderm microtubule-associated protein first beta-propeller / Cilia- and flagella-associated protein 77 / Cilia- and flagella-associated protein 77 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 141 / : / : / Meiosis-specific nuclear structural protein 1 / Cilia- and flagella-associated protein 45 / NDPK7, second NDPk domain / Cilia- and flagella- associated protein 210 / CFAP53/TCHP / Trichohyalin-plectin-homology domain / Trichohyalin-plectin-homology domain / RIB43A / RIB43A / DM10 domain / EF-hand domain-containing protein EFHC1/EFHC2/EFHB / DM10 domain / DM10 domain profile. / Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases. / Enkurin domain / : / Calmodulin-binding / Enkurin domain profile. / : / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / Parkin co-regulated protein / Parkin co-regulated protein / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / Alpha tubulin / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / EF-hand domain pair / WD domain, G-beta repeat / Armadillo-type fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Parkin co-regulated protein / Tubulin beta chain / Uncharacterized protein / IQ calmodulin-binding motif family protein / RIIa domain-containing protein / LOC402794 protein, putative / Nucleoside diphosphate kinase / Tubulin alpha chain ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Parkin co-regulated protein / Tubulin beta chain / Uncharacterized protein / IQ calmodulin-binding motif family protein / RIIa domain-containing protein / LOC402794 protein, putative / Nucleoside diphosphate kinase / Tubulin alpha chain / Transcription factor 2B, putative / Trichohyalin-plectin-homology domain-containing protein / Parkin co-regulated protein / Cilia- and flagella-associated protein 45 / Uncharacterized protein / Uncharacterized protein / Meiosis-specific nuclear structural protein 1 / Uncharacterized protein / Uncharacterized protein / Cilia- and flagella-associated protein 52 / Flagellar protofilament ribbon protein, putative / Cilia- and flagella-associated protein 53 / EF hand family protein / MGC84469 protein, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsStevens, A. / Zhou, H.Z. / Kashyap, S. / Crofut, E.J.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1S10 OD018111 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10 RR23057 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI103182 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R33 AI119721 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structures of Native Doublet Microtubules from Trichomonas vaginalis Reveal Parasite-Specific Proteins.
Authors: Alexander Stevens / Saarang Kashyap / Ethan H Crofut / Shuqi E Wang / Katherine A Muratore / Patricia J Johnson / Z Hong Zhou /
Abstract: 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- ...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.
History
DepositionAug 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Tubulin beta chain
A: FAP21
Fi: Tubulin alpha chain
Fj: Tubulin alpha chain
Fk: Tubulin alpha chain
Fl: Tubulin beta chain
Fm: Tubulin beta chain
Fn: Tubulin beta chain
Fo: Tubulin beta chain
Fp: Tubulin beta chain
Fq: Tubulin beta chain
Fr: Tubulin beta chain
Fs: Tubulin beta chain
A0: Tubulin beta chain
Ft: Tubulin beta chain
Fu: Tubulin beta chain
Fv: Tubulin beta chain
Fw: Tubulin beta chain
Fx: Tubulin beta chain
Fy: Tubulin beta chain
Fz: Tubulin beta chain
G: IQ calmodulin-binding motif family protein
G0: Flagellar protofilament ribbon protein, putative
G1: Tubulin alpha chain
G2: Tubulin alpha chain
G3: Tubulin alpha chain
G4: Tubulin alpha chain
G5: Tubulin alpha chain
G6: Tubulin alpha chain
G7: Flagellar protofilament ribbon protein, putative
G8: Flagellar protofilament ribbon protein, putative
G9: Flagellar protofilament ribbon protein, putative
GA: Tubulin alpha chain
GB: Tubulin alpha chain
GC: Tubulin alpha chain
GD: Tubulin alpha chain
GE: Tubulin alpha chain
A1: Tubulin alpha chain
GF: Tubulin alpha chain
GG: Tubulin alpha chain
GH: Tubulin beta chain
GI: Tubulin alpha chain
GJ: Tubulin alpha chain
GK: Tubulin alpha chain
GL: Tubulin alpha chain
GM: Tubulin alpha chain
GN: Tubulin alpha chain
GO: Tubulin alpha chain
GP: Tubulin alpha chain
GQ: Tubulin alpha chain
GR: Tubulin alpha chain
GS: Tubulin alpha chain
GT: Tubulin alpha chain
GU: Tubulin beta chain
GV: Tubulin beta chain
GW: Tubulin beta chain
GX: Tubulin beta chain
GY: Tubulin beta chain
GZ: Tubulin beta chain
Ga: Tubulin beta chain
Gb: Tubulin beta chain
Gc: Tubulin beta chain
Gd: Tubulin beta chain
Ge: Tubulin beta chain
Gf: Tubulin beta chain
Gg: Tubulin beta chain
Gh: Tubulin beta chain
Gi: Tubulin beta chain
Gj: Tubulin beta chain
Gk: Tubulin beta chain
A2: Tubulin alpha chain
Gl: Tubulin alpha chain
Gm: Tubulin beta chain
Gn: Tubulin alpha chain
Go: Tubulin alpha chain
Gp: Tubulin alpha chain
Gq: Tubulin alpha chain
Gr: Tubulin alpha chain
Gs: Tubulin alpha chain
Gt: Tubulin alpha chain
Gu: Tubulin alpha chain
Gv: Tubulin alpha chain
Gw: Tubulin alpha chain
Gx: Tubulin alpha chain
Gy: Tubulin alpha chain
Gz: Tubulin alpha chain
H: TvFAP40
HA: Parkin co-regulated protein
HB: Parkin co-regulated protein
HC: Parkin co-regulated protein
HD: Parkin co-regulated protein
I: Cilia- and flagella-associated protein 45
M: Cilia- and flagella-associated protein 20
N: Cilia- and flagella-associated protein 53
O: Tubulin beta chain
P: Tubulin beta chain
Q: Tubulin alpha chain
R: Tubulin alpha chain
S: Tubulin alpha chain
T: Tubulin alpha chain
U: Tubulin beta chain
V: Tubulin alpha chain
W: Tubulin alpha chain
X: Tubulin beta chain
A3: Tubulin beta chain
Y: Tubulin alpha chain
Z: Tubulin alpha chain
a: Tubulin alpha chain
b: Tubulin alpha chain
c: Tubulin alpha chain
d: Tubulin alpha chain
e: Tubulin alpha chain
f: Tubulin alpha chain
g: Tubulin alpha chain
h: Tubulin alpha chain
i: Tubulin alpha chain
j: Tubulin alpha chain
k: Tubulin alpha chain
l: Tubulin alpha chain
m: Tubulin beta chain
n: Tubulin beta chain
o: Tubulin alpha chain
p: Tubulin alpha chain
A4: Tubulin alpha chain
q: Tubulin alpha chain
r: Tubulin beta chain
s: Tubulin alpha chain
t: Tubulin alpha chain
u: Tubulin alpha chain
v: Tubulin alpha chain
w: Tubulin alpha chain
x: Tubulin alpha chain
y: Tubulin alpha chain
z: Tubulin alpha chain
A5: Tubulin alpha chain
A6: Tubulin alpha chain
A7: Tubulin alpha chain
A8: Tubulin alpha chain
A9: Tubulin alpha chain
AA: Tubulin beta chain
AB: Tubulin beta chain
AC: Tubulin beta chain
AD: Tubulin beta chain
AE: Tubulin beta chain
AF: Tubulin beta chain
AG: Tubulin beta chain
AH: Tubulin beta chain
AI: Tubulin alpha chain
AJ: Tubulin alpha chain
AK: Tubulin alpha chain
1: Tubulin alpha chain
AL: Tubulin beta chain
AM: Tubulin beta chain
AN: Tubulin beta chain
AO: Tubulin beta chain
AP: Tubulin beta chain
AQ: Tubulin beta chain
AR: Tubulin beta chain
AS: Tubulin beta chain
AT: Tubulin beta chain
AU: Tubulin beta chain
AV: Tubulin beta chain
AW: Tubulin beta chain
AX: Tubulin beta chain
AY: Tubulin beta chain
AZ: Tubulin beta chain
Aa: Tubulin beta chain
Ab: Tubulin beta chain
Ac: Tubulin beta chain
Ad: Tubulin beta chain
Ae: Tubulin beta chain
Af: Tubulin beta chain
Ag: Tubulin beta chain
Ah: Tubulin beta chain
Ai: Tubulin beta chain
Aj: Tubulin alpha chain
Ak: Tubulin alpha chain
Al: Tubulin alpha chain
Am: Tubulin beta chain
An: Tubulin beta chain
Ao: Tubulin beta chain
Ap: Tubulin beta chain
Aq: Tubulin beta chain
Ar: Tubulin beta chain
As: Tubulin beta chain
At: Tubulin beta chain
Au: Tubulin beta chain
Av: Tubulin beta chain
2: Tubulin alpha chain
Aw: Tubulin alpha chain
Ax: Tubulin alpha chain
Ay: Tubulin alpha chain
Az: Tubulin beta chain
B: Trichohyalin-plectin-homology domain-containing protein
B0: Tubulin alpha chain
B1: Tubulin alpha chain
B2: Tubulin alpha chain
B3: Tubulin alpha chain
B4: Tubulin alpha chain
B5: Tubulin alpha chain
B6: Tubulin alpha chain
B7: Tubulin alpha chain
B8: Tubulin alpha chain
B9: Tubulin alpha chain
BA: Tubulin beta chain
BB: Tubulin beta chain
BC: Tubulin beta chain
BD: Tubulin beta chain
BE: Tubulin beta chain
BF: Tubulin beta chain
BG: Tubulin beta chain
BH: Tubulin beta chain
BI: Tubulin alpha chain
BJ: Tubulin alpha chain
BK: Tubulin alpha chain
BL: Tubulin alpha chain
BM: Tubulin alpha chain
BN: Tubulin alpha chain
BO: Tubulin alpha chain
3: Tubulin alpha chain
BP: Tubulin alpha chain
BQ: Tubulin alpha chain
BR: Tubulin alpha chain
BS: Tubulin alpha chain
BT: Tubulin alpha chain
BU: Tubulin alpha chain
BV: Tubulin alpha chain
BW: Tubulin beta chain
BX: Tubulin alpha chain
BY: Tubulin alpha chain
BZ: Tubulin beta chain
Ba: Tubulin beta chain
Bb: Tubulin beta chain
Bc: Tubulin alpha chain
Bd: Tubulin alpha chain
Be: Tubulin beta chain
Bf: Tubulin beta chain
Bg: Tubulin beta chain
Bh: Tubulin beta chain
Bi: Tubulin beta chain
Bj: Tubulin beta chain
Bk: Tubulin beta chain
Bl: Tubulin beta chain
Bm: Tubulin beta chain
Bn: Tubulin beta chain
Bo: Tubulin beta chain
Bp: Tubulin beta chain
Bq: Tubulin beta chain
Br: Tubulin beta chain
Bs: Tubulin beta chain
Bt: Tubulin beta chain
Bu: Tubulin alpha chain
4: Tubulin alpha chain
Bv: Tubulin alpha chain
Bw: Tubulin alpha chain
Bx: Tubulin alpha chain
By: Tubulin alpha chain
Bz: Tubulin alpha chain
C: Trichohyalin-plectin-homology domain-containing protein
C1: Cilia- and flagella-associated protein 20
C2: Parkin co-regulated protein
C3: Parkin co-regulated protein
CA: Tubulin alpha chain
CB: Tubulin alpha chain
CC: Enkurin
CD: IQ calmodulin-binding motif family protein
CE: TvFAP40
CF: FAP77
CG: EF hand family protein
CH: Cilia- and flagella-associated protein 52
CI: Cilia- and flagella-associated protein 20
CJ: Cilia- and flagella-associated protein 45
CK: Cilia- and flagella-associated protein 45
CL: Cilia- and flagella-associated protein 45
CM: Nucleoside diphosphate kinase
CN: FAP161
CO: Nucleoside diphosphate kinase
CP: Nucleoside diphosphate kinase
CQ: FAP161
CR: RIIa domain-containing protein
CS: FAP12
CT: Meiosis-specific nuclear structural protein 1
CU: Meiosis-specific nuclear structural protein 1
CV: Cilia- and flagella-associated protein 53
CW: MGC84469 protein, putative
CX: Cilia- and flagella-associated protein 53
CY: Enkurin
CZ: Enkurin
Ca: IQ calmodulin-binding motif family protein
Cb: IQ calmodulin-binding motif family protein
Cc: FAP77
Cd: Cilia- and flagella-associated protein 52
Ce: Cilia- and flagella-associated protein 52
Cf: FAP77
Cg: FAP77
Ch: EF hand family protein
Ci: EF hand family protein
Cj: EF hand family protein
Ck: EF hand family protein
Cl: EF hand family protein
Cm: TvFAP40
Cn: TvFAP40
Co: MGC84469 protein, putative
Cp: MGC84469 protein, putative
Cq: MGC84469 protein, putative
Cr: MGC84469 protein, putative
Cs: MGC84469 protein, putative
Ct: MGC84469 protein, putative
Cu: Cilia- and flagella-associated protein 20
Cv: Cilia- and flagella-associated protein 20
Cw: Cilia- and flagella-associated protein 20
Cx: Cilia- and flagella-associated protein 20
Cy: Cilia- and flagella-associated protein 20
Cz: Parkin co-regulated protein
D: Cilia- and flagella-associated protein 52
DL: Tubulin beta chain
5: Tubulin alpha chain
DM: Tubulin beta chain
DN: Tubulin beta chain
DO: Tubulin beta chain
DP: Tubulin beta chain
DQ: Tubulin beta chain
DR: Tubulin beta chain
DS: Tubulin beta chain
DT: Tubulin beta chain
DU: Tubulin beta chain
DV: Tubulin beta chain
DW: Tubulin beta chain
DX: Tubulin beta chain
DY: Tubulin beta chain
DZ: Tubulin beta chain
Da: Tubulin beta chain
Db: Tubulin beta chain
Dc: Tubulin beta chain
Dd: Tubulin beta chain
De: Tubulin beta chain
Df: Tubulin beta chain
Dg: Tubulin beta chain
Dh: Tubulin beta chain
Di: Tubulin beta chain
Dj: Tubulin beta chain
Dk: Tubulin beta chain
Dq: Tubulin beta chain
Dr: Tubulin beta chain
Ds: Tubulin beta chain
Dt: Tubulin beta chain
Du: Tubulin beta chain
Dv: Tubulin beta chain
Dw: Tubulin beta chain
Dx: Tubulin beta chain
E: EF hand family protein
E0: Tubulin beta chain
E1: Tubulin alpha chain
E2: Tubulin alpha chain
E3: Tubulin alpha chain
6: Tubulin alpha chain
E4: Tubulin alpha chain
E5: Tubulin alpha chain
E6: Tubulin alpha chain
E7: Tubulin alpha chain
E8: Tubulin alpha chain
E9: Tubulin beta chain
EL: Tubulin beta chain
EM: Tubulin beta chain
EN: Tubulin beta chain
EO: Tubulin beta chain
EP: Tubulin beta chain
EQ: Tubulin beta chain
ER: Tubulin beta chain
ES: Tubulin beta chain
ET: Tubulin beta chain
EU: Tubulin beta chain
EV: Tubulin beta chain
EW: Tubulin beta chain
EX: Tubulin beta chain
EY: Tubulin beta chain
EZ: Tubulin beta chain
Ea: Tubulin beta chain
Eb: Tubulin beta chain
Ec: Tubulin beta chain
Ed: Tubulin beta chain
Ee: Tubulin alpha chain
Ef: Tubulin beta chain
Eg: Tubulin alpha chain
Eh: Tubulin alpha chain
Ei: Tubulin alpha chain
Ej: Tubulin alpha chain
Ek: Tubulin alpha chain
El: Tubulin alpha chain
7: Tubulin beta chain
Em: Tubulin alpha chain
En: Tubulin alpha chain
Eo: Tubulin alpha chain
Ep: Tubulin alpha chain
Eq: Tubulin alpha chain
Er: Tubulin alpha chain
Es: Tubulin alpha chain
Et: Tubulin alpha chain
Eu: Tubulin alpha chain
Ev: Tubulin beta chain
Ew: Tubulin alpha chain
Ex: Tubulin alpha chain
Ey: Tubulin alpha chain
Ez: Tubulin alpha chain
F: Enkurin
F0: Tubulin alpha chain
F1: Tubulin beta chain
F2: Tubulin beta chain
F3: Tubulin alpha chain
8: Tubulin beta chain
F4: Tubulin beta chain
F5: Tubulin alpha chain
F6: Tubulin alpha chain
F7: Tubulin alpha chain
F8: Tubulin alpha chain
F9: Tubulin alpha chain
FA: Tubulin beta chain
FB: Tubulin beta chain
FC: Tubulin beta chain
FD: Tubulin beta chain
FE: Tubulin beta chain
FF: Tubulin beta chain
FG: Tubulin beta chain
FH: Tubulin beta chain
FI: Tubulin beta chain
FJ: Tubulin beta chain
FK: Tubulin beta chain
FL: Tubulin beta chain
FM: Tubulin alpha chain
FN: Tubulin beta chain
FO: Tubulin alpha chain
FP: Tubulin alpha chain
9: Tubulin beta chain
FQ: Tubulin alpha chain
FR: Tubulin alpha chain
FS: Tubulin alpha chain
FT: Tubulin alpha chain
FU: Tubulin alpha chain
FV: Tubulin alpha chain
FW: Tubulin alpha chain
FX: Tubulin alpha chain
FY: Tubulin alpha chain
FZ: Tubulin alpha chain
Fa: Tubulin alpha chain
Fb: Tubulin alpha chain
Fc: Tubulin alpha chain
Fd: Tubulin alpha chain
Fe: Tubulin alpha chain
Ff: Tubulin alpha chain
Fg: Tubulin alpha chain
Fh: Tubulin alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,653,3091018
Polymers22,465,730451
Non-polymers187,579567
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 16 types, 425 molecules 0FlFmFnFoFpFqFrFsA0FtFuFvFwFxFyFzGHGUGVGWGXGYGZGaGbGcGdGeGf...

#1: Protein ...
Tubulin beta chain


Mass: 50001.035 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2DC16
#2: Protein FAP21


Mass: 43119.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2F5C9
#3: Protein ...
Tubulin alpha chain


Mass: 50166.504 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2E8B1
#4: Protein
IQ calmodulin-binding motif family protein


Mass: 35480.570 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2DUL4
#5: Protein
Flagellar protofilament ribbon protein, putative


Mass: 46130.445 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2FZ95
#6: Protein
TvFAP40


Mass: 43785.008 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2DSS2
#11: Protein Trichohyalin-plectin-homology domain-containing protein


Mass: 54623.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2EFC9
#13: Protein
Enkurin


Mass: 28259.299 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2E7V9
#14: Protein
FAP77


Mass: 32057.600 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2FTW1
#15: Protein
EF hand family protein


Mass: 107833.578 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2G843
#17: Protein Nucleoside diphosphate kinase


Mass: 42253.996 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2E829, nucleoside-diphosphate kinase
#18: Protein FAP161


Mass: 28401.012 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2FL25
#19: Protein RIIa domain-containing protein


Mass: 8949.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2DVD4
#20: Protein FAP12


Mass: 12391.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2F1C6
#21: Protein Meiosis-specific nuclear structural protein 1


Mass: 59697.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2FH94
#22: Protein
MGC84469 protein, putative


Mass: 68197.602 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2GCC1

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Parkin co-regulated ... , 2 types, 7 molecules HAHBHCHDC2C3Cz

#7: Protein
Parkin co-regulated protein


Mass: 27685.980 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2EJQ5
#12: Protein Parkin co-regulated protein


Mass: 27272.264 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2DAX1

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Cilia- and flagella-associated protein ... , 4 types, 19 molecules ICJCKCLMC1CICuCvCwCxCyNCVCXCHCdCeD

#8: Protein
Cilia- and flagella-associated protein 45


Mass: 55181.746 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2ETR1
#9: Protein
Cilia- and flagella-associated protein 20


Mass: 22837.334 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2EAE1
#10: Protein Cilia- and flagella-associated protein 53


Mass: 57844.656 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2G223
#16: Protein
Cilia- and flagella-associated protein 52


Mass: 65743.289 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis G3 (eukaryote) / References: UniProt: A2FVE3

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Non-polymers , 3 types, 567 molecules

#23: Chemical...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 191 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#24: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 188 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#25: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 188 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: doublet microtubule with microtubule inner proteins / Type: COMPLEX / Details: from T. vaginalis / Entity ID: #1, #3 / Source: NATURAL
Molecular weightValue: 20.1 MDa / Experimental value: NO
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote) / Organelle: flagella
Buffer solutionpH: 7.4
Details: 150 mM NaCl, 50 mM 325 Tris, 2 mM MgCl2, 1 mM DTT, 5 mM ATP 2 x complete protease inhibitor, pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMtrisC4H11NO31
31 mMdithiothreitolC4H10O2S21
45 mMadenosine triphosphateC10H16N5O13P31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 941307
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: OTHER / Num. of particles: 409692 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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