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- PDB-9cpc: Atomic model of porcine brain ventricles cilia doublet microtubul... -

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基本情報

登録情報
データベース: PDB / ID: 9cpc
タイトルAtomic model of porcine brain ventricles cilia doublet microtubule (48-nm periodicity)
要素
  • (Chromosome 1 ...) x 2
  • (Cilia and flagella associated protein ...) x 6
  • (Cilia- and flagella-associated protein ...) x 4
  • (Ciliary microtubule inner protein ...) x 2
  • (EF-hand domain ...) x 2
  • (Outer dynein ...) x 2
  • (Tektin) x 4
  • Armadillo repeat-containing protein 4 isoform 1
  • CFAP107/C1orf158
  • Cilia-and flagella-associated protein 96
  • Coiled-coil domain-containing protein 114 isoform X2
  • EF-hand calcium binding domain 1
  • EF-hand domain-containing family member C2
  • EFCAB6
  • Enkurin
  • Meiosis-specific nuclear structural protein 1
  • Nucleoside diphosphate kinase homolog 7
  • Parkin coregulated
  • Piercer of microtubule wall 1
  • Protein Flattop
  • RIB43A domain with coiled-coils 2
  • RIB43A-like with coiled-coils protein 1
  • Sperm acrosome associated 9
  • Sperm-associated antigen 8 isoform 1
  • Tubulin alpha chain
  • Tubulin beta chain
キーワードSTRUCTURAL PROTEIN / axoneme / cilia / microtubule / dynein / brain ventricle / doublet microtubule (DMT)
機能・相同性
機能・相同性情報


outer dynein arm docking complex / regulation of cilium beat frequency / determination of heart left/right asymmetry / protein localization to motile cilium / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / mucociliary clearance ...outer dynein arm docking complex / regulation of cilium beat frequency / determination of heart left/right asymmetry / protein localization to motile cilium / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / mucociliary clearance / axonemal B tubule inner sheath / axonemal A tubule inner sheath / inner dynein arm assembly / regulation of calcineurin-NFAT signaling cascade / sperm axoneme assembly / regulation of microtubule nucleation / positive regulation of feeding behavior / outer dynein arm assembly / cilium-dependent cell motility / 9+0 non-motile cilium / sperm principal piece / regulation of cilium beat frequency involved in ciliary motility / cerebrospinal fluid circulation / epithelial cilium movement involved in extracellular fluid movement / 9+2 motile cilium / regulation of store-operated calcium entry / intraciliary transport / regulation of cilium assembly / axoneme assembly / microtubule sliding / ciliary transition zone / cilium movement / left/right axis specification / calcium ion sensor activity / axonemal microtubule / ciliary tip / gamma-tubulin ring complex / ventricular system development / ciliary rootlet / manchette / positive regulation of cilium assembly / seminiferous tubule development / flagellated sperm motility / UTP biosynthetic process / CTP biosynthetic process / determination of left/right symmetry / intermediate filament / positive regulation of cell motility / nucleoside diphosphate kinase activity / motile cilium / GTP biosynthetic process / ciliary base / receptor clustering / regulation of neuron projection development / cerebral cortex cell migration / microtubule organizing center / regulation of cell division / mitotic cytokinesis / homeostasis of number of cells / axoneme / cilium assembly / spermatid development / glial cell projection / alpha-tubulin binding / single fertilization / sperm flagellum / beta-tubulin binding / microtubule-based process / cytoplasmic microtubule / sperm midpiece / Hsp70 protein binding / 3'-5' exonuclease activity / centriole / acrosomal vesicle / lung development / cellular response to leukemia inhibitory factor / mitotic spindle organization / meiotic cell cycle / Hsp90 protein binding / G protein-coupled receptor binding / brain development / structural constituent of cytoskeleton / SH3 domain binding / centriolar satellite / microtubule cytoskeleton organization / multicellular organism growth / cell morphogenesis / spindle pole / mitotic spindle / intracellular protein localization / nuclear envelope / mitotic cell cycle / actin binding / heart development / cell body / microtubule cytoskeleton / vesicle / spermatogenesis / microtubule binding / gene expression
類似検索 - 分子機能
Outer dynein arm-docking complex subunit 4 / Protein of unknown function DUF4586 / Outer dynein arm-docking complex subunit 3 / Cilia-and flagella-associated protein 96 / FAM183 family / FAM183A and FAM183B related / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain / Cilia- and flagella-associated protein 107 ...Outer dynein arm-docking complex subunit 4 / Protein of unknown function DUF4586 / Outer dynein arm-docking complex subunit 3 / Cilia-and flagella-associated protein 96 / FAM183 family / FAM183A and FAM183B related / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain / Cilia- and flagella-associated protein 107 / : / : / : / Protein CFAP95 / ODAD1 central coiled coil region / Cilia- and flagella-associated protein 143 / Cilia and flagella associated protein 107 / Tektin / Cilia- and flagella-associated protein 276 / Sperm acrosome-associated protein 9 / : / Tektin family / Protein of unknown function (DUF3695) / Sperm acrosome-associated protein 9 / Uncharacterised protein FAM166/UPF0605 / Cilia- and flagella-associated protein 77 / Protein Flattop / Ciliary microtubule inner protein 2B-like / Cilia- and flagella-associated protein 77 / Flattop / Nucleoside diphosphate kinase 7 / Piercer of microtubule wall 1/2 / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 141 / EFHB C-terminal EF-hand domain / Nucleoside diphosphate kinase 7 N-terminal PH domain / 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 / Recoverin family / Parkin co-regulated protein / Parkin co-regulated protein / EF hand / 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 / HEAT repeats / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Tetratricopeptide repeat / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / TPR repeat profile. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tetratricopeptide repeats / 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 / Tetratricopeptide repeat / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile.
類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Cilia- and flagella-associated protein 53 / EF-hand domain-containing protein 1 / Cilia- and flagella-associated protein 45 / Outer dynein arm-docking complex subunit 2 / Sperm-associated antigen 8 isoform 1 / Tektin / Tektin / Chromosome 1 C15orf65 homolog ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Cilia- and flagella-associated protein 53 / EF-hand domain-containing protein 1 / Cilia- and flagella-associated protein 45 / Outer dynein arm-docking complex subunit 2 / Sperm-associated antigen 8 isoform 1 / Tektin / Tektin / Chromosome 1 C15orf65 homolog / Meiosis-specific nuclear structural protein 1 / Enkurin / EF-hand calcium binding domain 1 / Tektin / Cilia-and flagella-associated protein 96 / Tubulin beta chain / Tubulin alpha chain / Outer dynein arm docking complex subunit 3 / Cilia and flagella associated protein 161 / Parkin coregulated / Cilia and flagella associated protein 276 / Chromosome 1 C9orf135 homolog / Nucleoside diphosphate kinase homolog 7 / Cilia and flagella associated protein 141 / RIB43A-like with coiled-coils protein 1 / Sperm acrosome associated 9 / Tektin / Ciliary microtubule inner protein 2B / Protein Flattop / Uncharacterized protein / Ciliary microtubule inner protein 2B / Outer dynein arm-docking complex subunit 4 / Uncharacterized protein / EF-hand domain family member B / Cilia and flagella associated protein 77 / Cilia and flagella associated protein 210 / Cilia and flagella associated protein 144 / RIB43A domain with coiled-coils 2 / Cilia- and flagella-associated protein 52 / Cilia-and flagella-associated protein 20 / Coiled-coil domain-containing protein 114 isoform X2 / EF-hand domain-containing family member C2
類似検索 - 構成要素
生物種Sus scrofa (ブタ)
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: 3.65 Å
データ登録者Sun, C. / Zeng, J. / Zhang, R.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM138854 米国
引用ジャーナル: Nature / 年: 2025
タイトル: Structural diversity of axonemes across mammalian motile cilia.
著者: Miguel Ricardo Leung / Chen Sun / Jianwei Zeng / Jacob R Anderson / Qingwei Niu / Wei Huang / Willem E M Noteborn / Alan Brown / Tzviya Zeev-Ben-Mordehai / Rui Zhang /
要旨: Reproduction, development and homeostasis depend on motile cilia, whose rhythmic beating is powered by a microtubule-based molecular machine called the axoneme. Although an atomic model of the ...Reproduction, development and homeostasis depend on motile cilia, whose rhythmic beating is powered by a microtubule-based molecular machine called the axoneme. Although an atomic model of the axoneme is available for the alga Chlamydomonas reinhardtii, structures of mammalian axonemes are incomplete. Furthermore, we do not fully understand how molecular structures of axonemes vary across motile-ciliated cell types in the body. Here we use cryoelectron microscopy, cryoelectron tomography and proteomics to resolve the 96-nm modular repeat of axonemal doublet microtubules (DMTs) from both sperm flagella and epithelial cilia of the oviduct, brain ventricles and respiratory tract. We find that sperm DMTs are the most specialized, with epithelial cilia having only minor differences across tissues. We build a model of the mammalian sperm DMT, defining the positions and interactions of 181 proteins including 34 newly identified proteins. We elucidate the composition of radial spoke 3 and uncover binding sites of kinases associated with regeneration of ATP and regulation of ciliary motility. We discover a sperm-specific, axoneme-tethered T-complex protein ring complex (TRiC) chaperone that may contribute to construction or maintenance of the long flagella of mammalian sperm. We resolve axonemal dyneins in their prestroke states, illuminating conformational changes that occur during ciliary movement. Our results illustrate how elements of chemical and mechanical regulation are embedded within the axoneme, providing valuable resources for understanding the aetiology of ciliopathy and infertility, and exemplifying the discovery power of modern structural biology.
履歴
登録2024年7月18日登録サイト: RCSB / 処理サイト: RCSB
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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
1A: Armadillo repeat-containing protein 4 isoform 1
1B: Armadillo repeat-containing protein 4 isoform 1
1C: Outer dynein arm-docking complex subunit 4
1D: Outer dynein arm-docking complex subunit 4
1F: EF-hand calcium binding domain 1
1G: EF-hand calcium binding domain 1
1H: Coiled-coil domain-containing protein 114 isoform X2
1I: Coiled-coil domain-containing protein 114 isoform X2
1J: Coiled-coil domain-containing protein 114 isoform X2
1L: Outer dynein arm docking complex subunit 3
1M: Outer dynein arm docking complex subunit 3
1N: Outer dynein arm docking complex subunit 3
1P: EFCAB6
1Q: EFCAB6
1S: Cilia- and flagella-associated protein 52
1T: Cilia- and flagella-associated protein 52
1U: Cilia- and flagella-associated protein 52
1W: Cilia- and flagella-associated protein 45
1X: Cilia- and flagella-associated protein 45
1Y: Cilia- and flagella-associated protein 45
1Z: Cilia- and flagella-associated protein 45
2B: Cilia and flagella associated protein 210
2C: Cilia and flagella associated protein 210
2E: Cilia and flagella associated protein 276
2F: Cilia and flagella associated protein 276
2G: Cilia and flagella associated protein 276
2I: Enkurin
2J: Enkurin
2K: Enkurin
2M: Parkin coregulated
2N: Parkin coregulated
2O: Parkin coregulated
2P: Parkin coregulated
2Q: Parkin coregulated
2R: Parkin coregulated
2T: Cilia- and flagella-associated protein 20
2U: Cilia- and flagella-associated protein 20
2V: Cilia- and flagella-associated protein 20
2W: Cilia- and flagella-associated protein 20
2X: Cilia- and flagella-associated protein 20
3A: Protein Flattop
3B: Protein Flattop
3C: Protein Flattop
3E: Tektin
3F: Tektin
3G: Tektin
3H: Tektin
3J: Tektin
3K: Tektin
3L: Tektin
3M: Tektin
3O: Tektin
3P: Tektin
3Q: Tektin
3R: Tektin
3T: Tektin
3U: Tektin
3V: Tektin
3W: Tektin
3Y: RIB43A domain with coiled-coils 2
3Z: RIB43A domain with coiled-coils 2
4A: RIB43A-like with coiled-coils protein 1
4B: RIB43A-like with coiled-coils protein 1
4D: EF-hand domain containing 1
4E: EF-hand domain containing 1
4F: EF-hand domain containing 1
4H: EF-hand domain-containing family member C2
4I: EF-hand domain-containing family member C2
4J: EF-hand domain-containing family member C2
4K: EF-hand domain-containing family member C2
4M: Ciliary microtubule inner protein 2B
4N: Ciliary microtubule inner protein 2B
4O: Ciliary microtubule inner protein 2B
4P: Ciliary microtubule inner protein 2B
4Q: Ciliary microtubule inner protein 2B
4R: Ciliary microtubule inner protein 2B
4T: Sperm-associated antigen 8 isoform 1
4V: Nucleoside diphosphate kinase homolog 7
4W: Nucleoside diphosphate kinase homolog 7
4Y: Cilia and flagella associated protein 161
4Z: Cilia and flagella associated protein 161
5B: Chromosome 1 C9orf135 homolog
5D: Piercer of microtubule wall 1
5E: Piercer of microtubule wall 1
5G: Chromosome 1 C15orf65 homolog
5I: EF-hand domain family member B
5J: EF-hand domain family member B
5L: Cilia and flagella associated protein 141
5N: Meiosis-specific nuclear structural protein 1
5O: Meiosis-specific nuclear structural protein 1
5Q: Cilia- and flagella-associated protein 53
5R: Cilia- and flagella-associated protein 53
5T: CFAP107/C1orf158
5U: CFAP107/C1orf158
5W: Cilia and flagella associated protein 77
5X: Cilia and flagella associated protein 77
5Y: Cilia and flagella associated protein 77
5Z: Cilia and flagella associated protein 77
6A: Cilia and flagella associated protein 144
6C: Cilia-and flagella-associated protein 96
6D: Cilia-and flagella-associated protein 96
6F: Sperm acrosome associated 9
6G: Sperm acrosome associated 9
6H: Sperm acrosome associated 9
6I: Sperm acrosome associated 9
6J: Sperm acrosome associated 9
6K: Sperm acrosome associated 9
6L: Sperm acrosome associated 9
AA: Tubulin alpha chain
AB: Tubulin beta chain
AE: Tubulin alpha chain
AF: Tubulin alpha chain
AG: Tubulin alpha chain
AH: Tubulin alpha chain
AL: Tubulin beta chain
AM: Tubulin beta chain
AN: Tubulin beta chain
AO: Tubulin beta chain
AP: Tubulin beta chain
BA: Tubulin alpha chain
BB: Tubulin beta chain
BE: Tubulin alpha chain
BF: Tubulin alpha chain
BG: Tubulin alpha chain
BH: Tubulin alpha chain
BI: Tubulin alpha chain
BL: Tubulin beta chain
BM: Tubulin beta chain
BN: Tubulin beta chain
BO: Tubulin beta chain
BP: Tubulin beta chain
CA: Tubulin alpha chain
CB: Tubulin beta chain
CE: Tubulin alpha chain
CF: Tubulin alpha chain
CG: Tubulin alpha chain
CH: Tubulin alpha chain
CI: Tubulin alpha chain
CL: Tubulin beta chain
CM: Tubulin beta chain
CN: Tubulin beta chain
CO: Tubulin beta chain
CP: Tubulin beta chain
DA: Tubulin alpha chain
DB: Tubulin beta chain
DE: Tubulin alpha chain
DF: Tubulin alpha chain
DG: Tubulin alpha chain
DH: Tubulin alpha chain
DI: Tubulin alpha chain
DL: Tubulin beta chain
DM: Tubulin beta chain
DN: Tubulin beta chain
DO: Tubulin beta chain
DP: Tubulin beta chain
EA: Tubulin alpha chain
EB: Tubulin beta chain
EE: Tubulin alpha chain
EF: Tubulin alpha chain
EG: Tubulin alpha chain
EH: Tubulin alpha chain
EI: Tubulin alpha chain
EL: Tubulin beta chain
EM: Tubulin beta chain
EN: Tubulin beta chain
EO: Tubulin beta chain
EP: Tubulin beta chain
FA: Tubulin alpha chain
FB: Tubulin beta chain
FE: Tubulin alpha chain
FF: Tubulin alpha chain
FG: Tubulin alpha chain
FH: Tubulin alpha chain
FI: Tubulin alpha chain
FM: Tubulin beta chain
FN: Tubulin beta chain
FO: Tubulin beta chain
FP: Tubulin beta chain
GA: Tubulin alpha chain
GB: Tubulin beta chain
GE: Tubulin alpha chain
GF: Tubulin alpha chain
GG: Tubulin alpha chain
GH: Tubulin alpha chain
GI: Tubulin alpha chain
GM: Tubulin beta chain
GN: Tubulin beta chain
GO: Tubulin beta chain
GP: Tubulin beta chain
HA: Tubulin alpha chain
HB: Tubulin beta chain
HE: Tubulin alpha chain
HF: Tubulin alpha chain
HG: Tubulin alpha chain
HH: Tubulin alpha chain
HI: Tubulin alpha chain
HM: Tubulin beta chain
HN: Tubulin beta chain
HO: Tubulin beta chain
HP: Tubulin beta chain
HQ: Tubulin beta chain
IA: Tubulin alpha chain
IB: Tubulin beta chain
IE: Tubulin alpha chain
IF: Tubulin alpha chain
IG: Tubulin alpha chain
IH: Tubulin alpha chain
II: Tubulin alpha chain
IM: Tubulin beta chain
IN: Tubulin beta chain
IO: Tubulin beta chain
IP: Tubulin beta chain
IQ: Tubulin beta chain
JA: Tubulin alpha chain
JB: Tubulin beta chain
JD: Tubulin alpha chain
JE: Tubulin alpha chain
JF: Tubulin alpha chain
JG: Tubulin alpha chain
JH: Tubulin alpha chain
JL: Tubulin beta chain
JM: Tubulin beta chain
JN: Tubulin beta chain
JO: Tubulin beta chain
KA: Tubulin alpha chain
KB: Tubulin beta chain
KD: Tubulin alpha chain
KE: Tubulin alpha chain
KF: Tubulin alpha chain
KG: Tubulin alpha chain
KH: Tubulin alpha chain
KL: Tubulin beta chain
KM: Tubulin beta chain
KN: Tubulin beta chain
KO: Tubulin beta chain
KP: Tubulin beta chain
LA: Tubulin alpha chain
LB: Tubulin beta chain
LD: Tubulin alpha chain
LE: Tubulin alpha chain
LF: Tubulin alpha chain
LG: Tubulin alpha chain
LH: Tubulin alpha chain
LL: Tubulin beta chain
LM: Tubulin beta chain
LN: Tubulin beta chain
LO: Tubulin beta chain
LP: Tubulin beta chain
MA: Tubulin alpha chain
MB: Tubulin beta chain
MD: Tubulin alpha chain
ME: Tubulin alpha chain
MF: Tubulin alpha chain
MG: Tubulin alpha chain
MH: Tubulin alpha chain
ML: Tubulin beta chain
MM: Tubulin beta chain
MN: Tubulin beta chain
MO: Tubulin beta chain
MP: Tubulin beta chain
NA: Tubulin alpha chain
NB: Tubulin beta chain
ND: Tubulin alpha chain
NE: Tubulin alpha chain
NF: Tubulin alpha chain
NG: Tubulin alpha chain
NH: Tubulin alpha chain
NL: Tubulin beta chain
NM: Tubulin beta chain
NN: Tubulin beta chain
NO: Tubulin beta chain
NP: Tubulin beta chain
OA: Tubulin alpha chain
OB: Tubulin beta chain
OD: Tubulin alpha chain
OE: Tubulin alpha chain
OF: Tubulin alpha chain
OG: Tubulin alpha chain
OH: Tubulin alpha chain
OL: Tubulin beta chain
OM: Tubulin beta chain
ON: Tubulin beta chain
OO: Tubulin beta chain
OP: Tubulin beta chain
PA: Tubulin alpha chain
PB: Tubulin beta chain
PD: Tubulin alpha chain
PE: Tubulin alpha chain
PF: Tubulin alpha chain
PG: Tubulin alpha chain
PH: Tubulin alpha chain
PL: Tubulin beta chain
PM: Tubulin beta chain
PN: Tubulin beta chain
PO: Tubulin beta chain
PP: Tubulin beta chain
QA: Tubulin alpha chain
QB: Tubulin beta chain
QE: Tubulin alpha chain
QF: Tubulin alpha chain
QG: Tubulin alpha chain
QH: Tubulin alpha chain
QL: Tubulin beta chain
QM: Tubulin beta chain
QN: Tubulin beta chain
QO: Tubulin beta chain
QP: Tubulin beta chain
RA: Tubulin alpha chain
RB: Tubulin beta chain
RE: Tubulin alpha chain
RF: Tubulin alpha chain
RG: Tubulin alpha chain
RH: Tubulin alpha chain
RI: Tubulin alpha chain
RL: Tubulin beta chain
RM: Tubulin beta chain
RN: Tubulin beta chain
RO: Tubulin beta chain
RP: Tubulin beta chain
SA: Tubulin alpha chain
SB: Tubulin beta chain
SE: Tubulin alpha chain
SF: Tubulin alpha chain
SG: Tubulin alpha chain
SH: Tubulin alpha chain
SI: Tubulin alpha chain
SL: Tubulin beta chain
SM: Tubulin beta chain
SN: Tubulin beta chain
SO: Tubulin beta chain
SP: Tubulin beta chain
TA: Tubulin alpha chain
TB: Tubulin beta chain
TE: Tubulin alpha chain
TF: Tubulin alpha chain
TG: Tubulin alpha chain
TH: Tubulin alpha chain
TI: Tubulin alpha chain
TL: Tubulin beta chain
TM: Tubulin beta chain
TN: Tubulin beta chain
TO: Tubulin beta chain
TP: Tubulin beta chain
UA: Tubulin alpha chain
UB: Tubulin beta chain
UE: Tubulin alpha chain
UF: Tubulin alpha chain
UG: Tubulin alpha chain
UH: Tubulin alpha chain
UI: Tubulin alpha chain
UM: Tubulin beta chain
UN: Tubulin beta chain
UO: Tubulin beta chain
UP: Tubulin beta chain
VA: Tubulin alpha chain
VB: Tubulin beta chain
VF: Tubulin alpha chain
VG: Tubulin alpha chain
VH: Tubulin alpha chain
VI: Tubulin alpha chain
VJ: Tubulin alpha chain
VN: Tubulin beta chain
VO: Tubulin beta chain
VP: Tubulin beta chain
VQ: Tubulin beta chain
WA: Tubulin alpha chain
WB: Tubulin beta chain
WE: Tubulin alpha chain
WF: Tubulin alpha chain
WG: Tubulin alpha chain
WH: Tubulin alpha chain
WI: Tubulin alpha chain
WM: Tubulin beta chain
WN: Tubulin beta chain
WO: Tubulin beta chain
WP: Tubulin beta chain
WQ: Tubulin beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,796,804646
ポリマ－18,666,706377
非ポリマー130,098269
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 , 23種, 332分子 1A1B1F1G1H1I1J1P1Q2I2J2K2M2N2O2P2Q2R3A3B3C3E3F3G3H3J3K3L3M3O...

#1: タンパク質 Armadillo repeat-containing protein 4 isoform 1 / Outer dynein arm docking complex subunit 2


分子量: 116987.055 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A480NQN9
#3: タンパク質 EF-hand calcium binding domain 1


分子量: 29379.803 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A4X1U4E1
#4: タンパク質 Coiled-coil domain-containing protein 114 isoform X2 / Outer dynein arm docking complex subunit 1


分子量: 80337.516 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: I3LGU2
#6: タンパク質 EFCAB6


分子量: 167103.703 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ)
#11: タンパク質 Enkurin


分子量: 29949.805 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A4X1TZW7
#12: タンパク質
Parkin coregulated


分子量: 29412.234 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D0JJX5
#14: タンパク質 Protein Flattop / Cilia- and flagella-associated protein 126


分子量: 19236.705 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D1FAM0
#15: タンパク質
Tektin


分子量: 48432.867 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A4X1ULV5
#16: タンパク質
Tektin


分子量: 49973.676 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D0ZEV6
#17: タンパク質
Tektin


分子量: 56552.840 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A4X1SQE5
#18: タンパク質
Tektin


分子量: 52015.508 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A4X1SYW5
#19: タンパク質 RIB43A domain with coiled-coils 2


分子量: 45003.449 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: F1SM62
#20: タンパク質 RIB43A-like with coiled-coils protein 1


分子量: 44590.852 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D0YSQ9
#22: タンパク質
EF-hand domain-containing family member C2


分子量: 87254.148 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: K7GSU4
#25: タンパク質 Sperm-associated antigen 8 isoform 1


分子量: 50537.250 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A480VJN4
#26: タンパク質 Nucleoside diphosphate kinase homolog 7 / NDK 7


分子量: 42532.766 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D0SNF8
#29: タンパク質 Piercer of microtubule wall 1


分子量: 15692.243 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D1K3C6
#33: タンパク質 Meiosis-specific nuclear structural protein 1


分子量: 60768.789 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A4X1TJ85
#35: タンパク質 CFAP107/C1orf158


分子量: 23449.852 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D1WB49
#38: タンパク質 Cilia-and flagella-associated protein 96


分子量: 34594.367 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A4X1VW16
#39: タンパク質
Sperm acrosome associated 9


分子量: 25335.152 Da / 分子数: 7 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D0ZB69
#40: タンパク質 ...
Tubulin alpha chain


分子量: 49797.035 Da / 分子数: 136 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A5G2QX54
#41: タンパク質 ...
Tubulin beta chain


分子量: 49798.211 Da / 分子数: 133 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A5G2QGK1

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Outer dynein ... , 2種, 5分子 1C1D1L1M1N

#2: タンパク質 Outer dynein arm-docking complex subunit 4 / Tetratricopeptide repeat protein 25


分子量: 78707.766 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D1SCU2
#5: タンパク質 Outer dynein arm docking complex subunit 3


分子量: 72117.602 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A5G2RIE6

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Cilia- and flagella-associated protein ... , 4種, 14分子 1S1T1U1W1X1Y1Z2T2U2V2W2X5Q5R

#7: タンパク質 Cilia- and flagella-associated protein 52 / WD repeat-containing protein 16


分子量: 68199.891 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: F1SS88
#8: タンパク質
Cilia- and flagella-associated protein 45


分子量: 65621.914 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A480NP79
#13: タンパク質
Cilia- and flagella-associated protein 20


分子量: 22781.389 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: F2Z513
#34: タンパク質 Cilia- and flagella-associated protein 53


分子量: 62200.133 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A286ZZD2

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Cilia and flagella associated protein ... , 6種, 13分子 2B2C2E2F2G4Y4Z5L5W5X5Y5Z6A

#9: タンパク質 Cilia and flagella associated protein 210 / Coiled-coil domain-containing protein 173


分子量: 66292.844 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: F1S1V4
#10: タンパク質 Cilia and flagella associated protein 276


分子量: 19304.631 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D0NP25
#27: タンパク質 Cilia and flagella associated protein 161


分子量: 35381.199 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D0J8R7
#32: タンパク質 Cilia and flagella associated protein 141


分子量: 12197.253 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D0XUD8
#36: タンパク質
Cilia and flagella associated protein 77


分子量: 32726.729 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: F1S0U2
#37: タンパク質 Cilia and flagella associated protein 144 / Protein FAM183A


分子量: 16325.543 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: F1SFB7

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EF-hand domain ... , 2種, 5分子 4D4E4F5I5J

#21: タンパク質 EF-hand domain containing 1 / EF-hand domain-containing protein 1 isoform 1 / EF-hand domain-containing protein 1 isoform X1


分子量: 74113.344 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A480I608
#31: タンパク質 EF-hand domain family member B


分子量: 98402.180 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: F1RS61

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Ciliary microtubule inner protein ... , 2種, 6分子 4M4N4P4Q4R4O

#23: タンパク質
Ciliary microtubule inner protein 2B


分子量: 30596.564 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D1CRM3
#24: タンパク質 Ciliary microtubule inner protein 2B


分子量: 28407.986 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D1QC18

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Chromosome 1 ... , 2種, 2分子 5B5G

#28: タンパク質 Chromosome 1 C9orf135 homolog


分子量: 26817.912 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A8D0NZG3
#30: タンパク質 Chromosome 1 C15orf65 homolog


分子量: 13888.583 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A4X1TH04

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非ポリマー , 2種, 269分子

#42: 化合物...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


分子量: 523.180 Da / 分子数: 136 / 由来タイプ: 天然 / 式: C10H16N5O14P3 / 由来: (天然) Sus scrofa (ブタ) / タイプ: SUBJECT OF INVESTIGATION / コメント: GTP, エネルギー貯蔵分子*YM
#43: 化合物...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 133 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: GDP, エネルギー貯蔵分子*YM

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詳細

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

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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: FILAMENT / 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: cilia from porcine brain ventricles / タイプ: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#19, #21-#41, #20 / 由来: NATURAL
分子量実験値: NO
由来(天然)生物種: Sus scrofa (ブタ)
緩衝液pH: 7.4
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE

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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: TFS 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 / 最大 デフォーカス（公称値）: 2500 nm / 最小 デフォーカス（公称値）: 500 nm
撮影電子線照射量: 50 e/Å2
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)

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解析

CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 3.65 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 113809 / 対称性のタイプ: POINT

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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

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