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

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基本情報

登録情報
データベース: PDB / ID: 9d5n
タイトル48-nm doublet microtubule from Trichomonas vaginalis strain G3
要素
  • (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
キーワードSTRUCTURAL PROTEIN / doublet microtubule / tubulin / flagella
機能・相同性
機能・相同性情報


cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / axonemal microtubule / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / nucleoside diphosphate kinase activity / 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 / motile cilium / positive regulation of cell motility / nucleoside diphosphate kinase activity / 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 / hydrolase activity / calmodulin binding / ciliary basal body / cilium / GTPase activity / GTP binding / ATP binding / nucleus / cytoplasm
類似検索 - 分子機能
: / 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-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 / Armadillo-type fold / WD domain, G-beta repeat / 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
類似検索 - ドメイン・相同性
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
類似検索 - 構成要素
生物種Trichomonas vaginalis G3 (ちつほねまくむし)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.2 Å
データ登録者Stevens, A. / Zhou, H.Z. / Kashyap, S. / Crofut, E.J.
資金援助 米国, 6件
組織認可番号国
National Institutes of Health/Office of the Director1S10 OD018111 米国
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10 RR23057 米国
National Science Foundation (NSF, United States)DBI-1338135 米国
National Science Foundation (NSF, United States)DMR-1548924 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI103182 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R33 AI119721 米国
引用ジャーナル: Nat Commun / 年: 2025
タイトル: Structures of Native Doublet Microtubules from Trichomonas vaginalis Reveal Parasite-Specific Proteins.
著者: Alexander Stevens / Saarang Kashyap / Ethan H Crofut / Shuqi E Wang / Katherine A Muratore / Patricia J Johnson / Z Hong Zhou /
要旨: 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.
履歴
登録2024年8月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年5月14日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,653,3091018
ポリマ－22,465,730451
非ポリマー187,579567
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_5551

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要素

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タンパク質 , 16種, 425分子 0FlFmFnFoFpFqFrFsA0FtFuFvFwFxFyFzGHGUGVGWGXGYGZGaGbGcGdGeGf...

#1: タンパク質 ...
Tubulin beta chain


分子量: 50001.035 Da / 分子数: 191 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2DC16
#2: タンパク質 FAP21


分子量: 43119.344 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2F5C9
#3: タンパク質 ...
Tubulin alpha chain


分子量: 50166.504 Da / 分子数: 188 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2E8B1
#4: タンパク質
IQ calmodulin-binding motif family protein


分子量: 35480.570 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2DUL4
#5: タンパク質
Flagellar protofilament ribbon protein, putative


分子量: 46130.445 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2FZ95
#6: タンパク質
TvFAP40


分子量: 43785.008 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2DSS2
#11: タンパク質 Trichohyalin-plectin-homology domain-containing protein


分子量: 54623.988 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2EFC9
#13: タンパク質
Enkurin


分子量: 28259.299 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2E7V9
#14: タンパク質
FAP77


分子量: 32057.600 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2FTW1
#15: タンパク質
EF hand family protein


分子量: 107833.578 Da / 分子数: 7 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2G843
#17: タンパク質 Nucleoside diphosphate kinase


分子量: 42253.996 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2E829, nucleoside-diphosphate kinase
#18: タンパク質 FAP161


分子量: 28401.012 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2FL25
#19: タンパク質 RIIa domain-containing protein


分子量: 8949.297 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2DVD4
#20: タンパク質 FAP12


分子量: 12391.051 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2F1C6
#21: タンパク質 Meiosis-specific nuclear structural protein 1


分子量: 59697.285 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2FH94
#22: タンパク質
MGC84469 protein, putative


分子量: 68197.602 Da / 分子数: 7 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2GCC1

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Parkin co-regulated ... , 2種, 7分子 HAHBHCHDC2C3Cz

#7: タンパク質
Parkin co-regulated protein


分子量: 27685.980 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2EJQ5
#12: タンパク質 Parkin co-regulated protein


分子量: 27272.264 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2DAX1

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Cilia- and flagella-associated protein ... , 4種, 19分子 ICJCKCLMC1CICuCvCwCxCyNCVCXCHCdCeD

#8: タンパク質
Cilia- and flagella-associated protein 45


分子量: 55181.746 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2ETR1
#9: タンパク質
Cilia- and flagella-associated protein 20


分子量: 22837.334 Da / 分子数: 8 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2EAE1
#10: タンパク質 Cilia- and flagella-associated protein 53


分子量: 57844.656 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2G223
#16: タンパク質
Cilia- and flagella-associated protein 52


分子量: 65743.289 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Trichomonas vaginalis G3 (ちつほねまくむし)
参照: UniProt: A2FVE3

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非ポリマー , 3種, 567分子

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


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 191 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / コメント: GDP, エネルギー貯蔵分子*YM
#24: 化合物...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 188 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM
#25: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 188 / 由来タイプ: 合成 / 式: Mg

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詳細

研究の焦点であるリガンドがあるかN
Has protein modificationN

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: doublet microtubule with microtubule inner proteins / タイプ: COMPLEX / 詳細: from T. vaginalis / Entity ID: #1, #3 / 由来: NATURAL
分子量値: 20.1 MDa / 実験値: NO
由来(天然)生物種: Trichomonas vaginalis G3 (ちつほねまくむし)
Organelle: flagella
緩衝液pH: 7.4
詳細: 150 mM NaCl, 50 mM 325 Tris, 2 mM MgCl2, 1 mM DTT, 5 mM ATP 2 x complete protease inhibitor, pH 7.4
緩衝液成分
ID濃度名称式Buffer-ID
1150 mMsodium chlorideNaCl1
250 mMtrisC4H11NO31
31 mMdithiothreitolC4H10O2S21
45 mMadenosine triphosphateC10H16N5O13P31
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドの材料: COPPER / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R2/1
急速凍結装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE-PROPANE / 湿度: 100 % / 凍結前の試料温度: 281 K

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 倍率（公称値）: 81000 X / 最大 デフォーカス（公称値）: 2000 nm / 最小 デフォーカス（公称値）: 1200 nm / Calibrated defocus min: 1200 nm / 最大 デフォーカス（補正後）: 2000 nm / Cs: 2.7 mm / アライメント法: COMA FREE
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影電子線照射量: 45 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)

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解析

EMソフトウェア名称: PHENIX / バージョン: 1.21.1_5286 / カテゴリ: モデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
粒子像の選択選択した粒子像数: 941307
対称性点対称性: C1 (非対称)
3次元再構成解像度: 4.2 Å / 解像度の算出法: OTHER / 粒子像の数: 409692 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 3 / 対称性のタイプ: POINT
原子モデル構築プロトコル: FLEXIBLE FIT / 空間: REAL
原子モデル構築Source name: AlphaFold / タイプ: in silico model

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る