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- PDB-9cpb: Atomic model of bovine Fallopian tube cilia doublet microtubule (... -

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基本情報

登録情報
データベース: PDB / ID: 9cpb
タイトルAtomic model of bovine Fallopian tube cilia doublet microtubule (48-nm periodicity)
要素
  • (Cilia and flagella associated protein ...) x 5
  • (Cilia- and flagella-associated protein ...) x 2
  • (Ciliary microtubule associated protein ...) x 2
  • (Coiled-coil domain containing ...) x 2
  • (EF-hand domain ...) x 2
  • Armadillo repeat containing 4
  • CFAP141
  • CFAP276
  • CFAP95
  • Cilia-and flagella-associated protein 96
  • EF-hand calcium binding domain 6
  • EF-hand calcium-binding domain-containing protein 1
  • EFHC2
  • Enkurin, TRPC channel interacting protein
  • Meiosis-specific nuclear structural protein 1
  • Methyl-CpG binding domain protein 1
  • Nucleoside diphosphate kinase 7
  • Outer dynein arm-docking complex subunit 3
  • PACRG protein
  • Pierce1
  • Pierce2
  • Protein FAM166B
  • Protein Flattop
  • RIB43A-like with coiled-coils protein 2
  • Sperm acrosome associated 9
  • Sperm associated antigen 8
  • TTC25 protein
  • Tektin-1
  • Tektin-2
  • Tektin-3
  • Tektin-4
  • Tubulin alpha-1D chain
  • Tubulin beta-4B chain
  • Uncharacterized protein C1orf158 homolog
キーワードSTRUCTURAL PROTEIN / axoneme / cilia / microtubule / dynein / Fallopian tube / doublet microtubule (DMT)
機能・相同性
機能・相同性情報


outer dynein arm docking complex / protein localization to motile cilium / regulation of cilium movement / 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 / sperm flagellum assembly ...outer dynein arm docking complex / protein localization to motile cilium / regulation of cilium movement / 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 / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / regulation of flagellated sperm motility / protein polyglutamylation / regulation of calcineurin-NFAT signaling cascade / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / : / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / positive regulation of feeding behavior / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / outer dynein arm assembly / 9+0 non-motile cilium / COPI-dependent Golgi-to-ER retrograde traffic / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases activate IQGAPs / inner dynein arm assembly / cilium-dependent cell motility / cerebrospinal fluid circulation / regulation of cilium beat frequency involved in ciliary motility / RHO GTPases Activate Formins / 9+2 motile cilium / cilium movement involved in cell motility / MHC class II antigen presentation / regulation of store-operated calcium entry / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / acrosomal membrane / regulation of cilium assembly / axoneme assembly / cilium movement / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / calcium ion sensor activity / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / axonemal microtubule / Recruitment of NuMA to mitotic centrosomes / cilium organization / gamma-tubulin ring complex / ciliary rootlet / manchette / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / flagellated sperm motility / 3'-5'-DNA exonuclease activity / UTP biosynthetic process / CTP biosynthetic process / motile cilium / determination of left/right symmetry / DNA catabolic process / Neutrophil degranulation / nucleoside diphosphate kinase activity / positive regulation of cell motility / GTP biosynthetic process / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドデオキシリボヌクレアーゼ / AMP binding / ciliary base / regulation of neuron projection development / cerebral cortex cell migration / ciliary transition zone / mitotic cytokinesis / microtubule organizing center / cellular response to UV-C / regulation of cell division / cilium assembly / spermatid development / regulation of signal transduction / axoneme / single fertilization / glial cell projection / sperm flagellum / alpha-tubulin binding / beta-tubulin binding / intercellular bridge / cytoplasmic microtubule / lung development / Hsp70 protein binding / ciliary tip / acrosomal vesicle / mitotic spindle organization
類似検索 - 分子機能
Outer dynein arm-docking complex subunit 4 / Protein of unknown function DUF4541 / : / Cilia and flagella associated protein 90 / Protein of unknown function DUF4586 / Outer dynein arm-docking complex subunit 3 / Cilia-and flagella-associated protein 96 / DJBP, EF-hand domain / FAM183 family / EF-hand domain ...Outer dynein arm-docking complex subunit 4 / Protein of unknown function DUF4541 / : / Cilia and flagella associated protein 90 / Protein of unknown function DUF4586 / Outer dynein arm-docking complex subunit 3 / Cilia-and flagella-associated protein 96 / DJBP, EF-hand domain / FAM183 family / EF-hand domain / FAM183A and FAM183B related / Sperm-tail PG-rich repeat / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain / Cilia- and flagella-associated protein 107 / : / Sperm-tail PG-rich repeat / Protein CFAP95 / Cilia- and flagella-associated protein 143 / Cilia and flagella associated protein 107 / : / Echinoderm microtubule-associated protein first beta-propeller / Tektin / Cilia- and flagella-associated protein 276 / Sperm acrosome-associated protein 9 / : / : / : / Tektin family / Protein of unknown function (DUF3695) / Sperm acrosome-associated protein 9 / ODAD1 central coiled coil region / 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 / Cilia- and flagella-associated protein 161-like domain / : / : / 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 / EF-hand domain pair / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Tetratricopeptide repeat / TPR repeat region circular profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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.
類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Piercer of microtubule wall 2 protein / Cilia and flagella associated protein 77 / Cilia and flagella associated protein 90 / Sperm acrosome associated 9 / EF-hand domain-containing family member C2 / Ciliary microtubule associated protein 1C / EF-hand calcium binding domain 6 / Outer dynein arm-docking complex subunit 4 ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Piercer of microtubule wall 2 protein / Cilia and flagella associated protein 77 / Cilia and flagella associated protein 90 / Sperm acrosome associated 9 / EF-hand domain-containing family member C2 / Ciliary microtubule associated protein 1C / EF-hand calcium binding domain 6 / Outer dynein arm-docking complex subunit 4 / Parkin coregulated gene protein / Tektin-3 / Outer dynein arm-docking complex subunit 3 / Cilia- and flagella-associated protein 144 / Enkurin / Outer dynein arm-docking complex subunit 2 / Cilia- and flagella-associated protein 276 / Cilia- and flagella- associated protein 210 / Cilia- and flagella-associated protein 52 / EF-hand domain-containing protein 1 / Sperm-associated antigen 8 / EF-hand domain-containing family member B / Outer dynein arm-docking complex subunit 1 / Cilia-and flagella-associated protein 96 / Cilia- and flagella-associated protein 53 / Cilia- and flagella-associated protein 161 / Tubulin alpha-1D chain / Meiosis-specific nuclear structural protein 1 / Tektin-2 / Cilia- and flagella-associated protein 107 / Tektin-4 / Ciliary microtubule inner protein 2B / Tektin-1 / Calaxin / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 95 / RIB43A-like with coiled-coils protein 2 / Cilia- and flagella-associated protein 45 / Piercer of microtubule wall 1 protein / Tubulin beta-4B chain / Protein Flattop / Nucleoside diphosphate kinase 7 / Cilia- and flagella-associated protein 20
類似検索 - 構成要素
生物種Bos taurus (ウシ)
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: 3.52 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
改定 1.02024年10月30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
1A: Armadillo repeat containing 4
1D: Coiled-coil domain containing 114
1E: Coiled-coil domain containing 114
1F: Coiled-coil domain containing 114
1H: Coiled-coil domain containing 173
1I: Coiled-coil domain containing 173
1K: Uncharacterized protein C1orf158 homolog
1L: Uncharacterized protein C1orf158 homolog
1N: Protein Flattop
1O: Protein Flattop
1P: Protein Flattop
1R: CFAP141
1T: Cilia and flagella associated protein 161
1U: Cilia and flagella associated protein 161
1W: Cilia- and flagella-associated protein 20
1X: Cilia- and flagella-associated protein 20
1Y: Cilia- and flagella-associated protein 20
1Z: Cilia- and flagella-associated protein 20
2A: Cilia- and flagella-associated protein 20
2B: Cilia- and flagella-associated protein 20
2D: EF-hand domain family member B
2E: EF-hand domain family member B
2F: CFAP276
2G: CFAP276
2H: CFAP276
2J: Cilia and flagella associated protein 45
2K: Cilia and flagella associated protein 45
2L: Cilia and flagella associated protein 45
2M: Cilia and flagella associated protein 45
2O: Cilia and flagella associated protein 52
2P: Cilia and flagella associated protein 52
2Q: Cilia and flagella associated protein 52
2S: Methyl-CpG binding domain protein 1
2T: Methyl-CpG binding domain protein 1
2V: Cilia and flagella associated protein 77
2W: Cilia and flagella associated protein 77
2X: Cilia and flagella associated protein 77
2Y: Cilia and flagella associated protein 77
3A: CFAP95
3C: Cilia-and flagella-associated protein 96
3D: Cilia-and flagella-associated protein 96
3F: EF-hand calcium-binding domain-containing protein 1
3H: EF-hand calcium binding domain 6
3J: EF-hand domain containing 1
3K: EF-hand domain containing 1
3L: EF-hand domain containing 1
3N: EFHC2
3O: EFHC2
3P: EFHC2
3Q: EFHC2
3S: Enkurin, TRPC channel interacting protein
3T: Enkurin, TRPC channel interacting protein
3U: Enkurin, TRPC channel interacting protein
3V: Enkurin, TRPC channel interacting protein
3X: Protein FAM166B
3Y: Protein FAM166B
3Z: Protein FAM166B
4A: Protein FAM166B
4B: Protein FAM166B
4C: Protein FAM166B
4D: Cilia- and flagella-associated protein 144
4F: Meiosis-specific nuclear structural protein 1
4G: Meiosis-specific nuclear structural protein 1
4I: Nucleoside diphosphate kinase 7
4J: Nucleoside diphosphate kinase 7
4K: Outer dynein arm-docking complex subunit 3
4L: Outer dynein arm-docking complex subunit 3
4M: Outer dynein arm-docking complex subunit 3
4O: PACRG protein
4P: PACRG protein
4Q: PACRG protein
4R: PACRG protein
4S: PACRG protein
4T: PACRG protein
4V: Pierce1
4W: Pierce1
4Y: Pierce2
5A: RIB43A-like with coiled-coils protein 2
5B: RIB43A-like with coiled-coils protein 2
5D: Sperm acrosome associated 9
5E: Sperm acrosome associated 9
5F: Sperm acrosome associated 9
5G: Sperm acrosome associated 9
5H: Sperm acrosome associated 9
5I: Sperm acrosome associated 9
5J: Sperm acrosome associated 9
5L: Tektin-1
5M: Tektin-1
5N: Tektin-1
5O: Tektin-1
5Q: Tektin-2
5R: Tektin-2
5S: Tektin-2
5T: Tektin-2
5V: Tektin-2
5W: Tektin-2
5X: Tektin-2
5Y: Tektin-2
6A: Tektin-3
6B: Tektin-3
6C: Tektin-3
6D: Tektin-3
6E: Tektin-3
6F: Tektin-3
6G: Tektin-3
6H: Tektin-3
6I: Tektin-3
6J: Tektin-3
6K: Tektin-3
6L: Tektin-3
6M: Tektin-3
6N: Tektin-3
6P: Tektin-4
6Q: Tektin-4
6R: Tektin-4
6S: Tektin-4
6T: Tektin-4
6U: Tektin-4
6V: Tektin-4
6W: Tektin-4
6Y: TTC25 protein
6Z: TTC25 protein
7C: Ciliary microtubule associated protein 1A
7D: Ciliary microtubule associated protein 1A
7E: Ciliary microtubule associated protein 1A
7F: Ciliary microtubule associated protein 1A
7H: Ciliary microtubule associated protein 1C
7I: Ciliary microtubule associated protein 1C
7K: Cilia and flagella associated protein 90
7L: Cilia and flagella associated protein 90
7N: Sperm associated antigen 8
AB: Tubulin beta-4B chain
AC: Tubulin alpha-1D chain
AD: Tubulin beta-4B chain
AE: Tubulin alpha-1D chain
AF: Tubulin beta-4B chain
AG: Tubulin alpha-1D chain
AH: Tubulin beta-4B chain
AI: Tubulin alpha-1D chain
AJ: Tubulin beta-4B chain
AK: Tubulin alpha-1D chain
AL: Tubulin beta-4B chain
BB: Tubulin beta-4B chain
BC: Tubulin alpha-1D chain
BD: Tubulin beta-4B chain
BE: Tubulin alpha-1D chain
BF: Tubulin beta-4B chain
BG: Tubulin alpha-1D chain
BH: Tubulin beta-4B chain
BI: Tubulin alpha-1D chain
BJ: Tubulin beta-4B chain
BK: Tubulin alpha-1D chain
BL: Tubulin beta-4B chain
CB: Tubulin beta-4B chain
CC: Tubulin alpha-1D chain
CD: Tubulin beta-4B chain
CE: Tubulin alpha-1D chain
CF: Tubulin beta-4B chain
CG: Tubulin alpha-1D chain
CH: Tubulin beta-4B chain
CI: Tubulin alpha-1D chain
CJ: Tubulin beta-4B chain
CK: Tubulin alpha-1D chain
CL: Tubulin beta-4B chain
CM: Tubulin alpha-1D chain
DB: Tubulin beta-4B chain
DC: Tubulin alpha-1D chain
DD: Tubulin beta-4B chain
DE: Tubulin alpha-1D chain
DF: Tubulin beta-4B chain
DG: Tubulin alpha-1D chain
DH: Tubulin beta-4B chain
DI: Tubulin alpha-1D chain
DJ: Tubulin beta-4B chain
DK: Tubulin alpha-1D chain
DL: Tubulin beta-4B chain
DM: Tubulin alpha-1D chain
EC: Tubulin alpha-1D chain
ED: Tubulin beta-4B chain
EE: Tubulin alpha-1D chain
EF: Tubulin beta-4B chain
EG: Tubulin alpha-1D chain
EH: Tubulin beta-4B chain
EI: Tubulin alpha-1D chain
EJ: Tubulin beta-4B chain
EK: Tubulin alpha-1D chain
EL: Tubulin beta-4B chain
EM: Tubulin alpha-1D chain
FC: Tubulin alpha-1D chain
FD: Tubulin beta-4B chain
FE: Tubulin alpha-1D chain
FF: Tubulin beta-4B chain
FG: Tubulin alpha-1D chain
FH: Tubulin beta-4B chain
FI: Tubulin alpha-1D chain
FJ: Tubulin beta-4B chain
FK: Tubulin alpha-1D chain
FL: Tubulin beta-4B chain
FM: Tubulin alpha-1D chain
GC: Tubulin alpha-1D chain
GD: Tubulin beta-4B chain
GE: Tubulin alpha-1D chain
GF: Tubulin beta-4B chain
GG: Tubulin alpha-1D chain
GH: Tubulin beta-4B chain
GI: Tubulin alpha-1D chain
GJ: Tubulin beta-4B chain
GK: Tubulin alpha-1D chain
GL: Tubulin beta-4B chain
GM: Tubulin alpha-1D chain
HB: Tubulin beta-4B chain
HC: Tubulin alpha-1D chain
HD: Tubulin beta-4B chain
HE: Tubulin alpha-1D chain
HF: Tubulin beta-4B chain
HG: Tubulin alpha-1D chain
HH: Tubulin beta-4B chain
HI: Tubulin alpha-1D chain
HJ: Tubulin beta-4B chain
HK: Tubulin alpha-1D chain
HL: Tubulin beta-4B chain
HM: Tubulin alpha-1D chain
IC: Tubulin alpha-1D chain
ID: Tubulin beta-4B chain
IE: Tubulin alpha-1D chain
IF: Tubulin beta-4B chain
IG: Tubulin alpha-1D chain
IH: Tubulin beta-4B chain
II: Tubulin alpha-1D chain
IJ: Tubulin beta-4B chain
IK: Tubulin alpha-1D chain
IL: Tubulin beta-4B chain
IM: Tubulin alpha-1D chain
IN: Tubulin beta-4B chain
JC: Tubulin alpha-1D chain
JD: Tubulin beta-4B chain
JE: Tubulin alpha-1D chain
JF: Tubulin beta-4B chain
JG: Tubulin alpha-1D chain
JH: Tubulin beta-4B chain
JI: Tubulin alpha-1D chain
JJ: Tubulin beta-4B chain
JK: Tubulin alpha-1D chain
JL: Tubulin beta-4B chain
JM: Tubulin alpha-1D chain
KC: Tubulin alpha-1D chain
KD: Tubulin beta-4B chain
KE: Tubulin alpha-1D chain
KF: Tubulin beta-4B chain
KG: Tubulin alpha-1D chain
KH: Tubulin beta-4B chain
KI: Tubulin alpha-1D chain
KJ: Tubulin beta-4B chain
KK: Tubulin alpha-1D chain
KL: Tubulin beta-4B chain
KM: Tubulin alpha-1D chain
KN: Tubulin beta-4B chain
LC: Tubulin alpha-1D chain
LD: Tubulin beta-4B chain
LE: Tubulin alpha-1D chain
LF: Tubulin beta-4B chain
LG: Tubulin alpha-1D chain
LH: Tubulin beta-4B chain
LI: Tubulin alpha-1D chain
LJ: Tubulin beta-4B chain
LK: Tubulin alpha-1D chain
LL: Tubulin beta-4B chain
LM: Tubulin alpha-1D chain
LN: Tubulin beta-4B chain
MC: Tubulin alpha-1D chain
MD: Tubulin beta-4B chain
ME: Tubulin alpha-1D chain
MF: Tubulin beta-4B chain
MG: Tubulin alpha-1D chain
MH: Tubulin beta-4B chain
MI: Tubulin alpha-1D chain
MJ: Tubulin beta-4B chain
MK: Tubulin alpha-1D chain
ML: Tubulin beta-4B chain
MM: Tubulin alpha-1D chain
MN: Tubulin beta-4B chain
NA: Tubulin alpha-1D chain
NB: Tubulin beta-4B chain
NC: Tubulin alpha-1D chain
ND: Tubulin beta-4B chain
NE: Tubulin alpha-1D chain
NF: Tubulin beta-4B chain
NG: Tubulin alpha-1D chain
NH: Tubulin beta-4B chain
NI: Tubulin alpha-1D chain
NJ: Tubulin beta-4B chain
NK: Tubulin alpha-1D chain
NL: Tubulin beta-4B chain
OA: Tubulin alpha-1D chain
OB: Tubulin beta-4B chain
OC: Tubulin alpha-1D chain
OD: Tubulin beta-4B chain
OE: Tubulin alpha-1D chain
OF: Tubulin beta-4B chain
OG: Tubulin alpha-1D chain
OH: Tubulin beta-4B chain
OI: Tubulin alpha-1D chain
OJ: Tubulin beta-4B chain
OK: Tubulin alpha-1D chain
OL: Tubulin beta-4B chain
PA: Tubulin alpha-1D chain
PB: Tubulin beta-4B chain
PC: Tubulin alpha-1D chain
PD: Tubulin beta-4B chain
PE: Tubulin alpha-1D chain
PF: Tubulin beta-4B chain
PG: Tubulin alpha-1D chain
PH: Tubulin beta-4B chain
PI: Tubulin alpha-1D chain
PJ: Tubulin beta-4B chain
PK: Tubulin alpha-1D chain
PL: Tubulin beta-4B chain
QB: Tubulin beta-4B chain
QC: Tubulin alpha-1D chain
QD: Tubulin beta-4B chain
QE: Tubulin alpha-1D chain
QF: Tubulin beta-4B chain
QG: Tubulin alpha-1D chain
QH: Tubulin beta-4B chain
QI: Tubulin alpha-1D chain
QJ: Tubulin beta-4B chain
QK: Tubulin alpha-1D chain
QL: Tubulin beta-4B chain
RB: Tubulin beta-4B chain
RC: Tubulin alpha-1D chain
RD: Tubulin beta-4B chain
RE: Tubulin alpha-1D chain
RF: Tubulin beta-4B chain
RG: Tubulin alpha-1D chain
RH: Tubulin beta-4B chain
RI: Tubulin alpha-1D chain
RJ: Tubulin beta-4B chain
RK: Tubulin alpha-1D chain
RL: Tubulin beta-4B chain
SC: Tubulin alpha-1D chain
SD: Tubulin beta-4B chain
SE: Tubulin alpha-1D chain
SF: Tubulin beta-4B chain
SG: Tubulin alpha-1D chain
SH: Tubulin beta-4B chain
SI: Tubulin alpha-1D chain
SJ: Tubulin beta-4B chain
SK: Tubulin alpha-1D chain
SL: Tubulin beta-4B chain
SM: Tubulin alpha-1D chain
TC: Tubulin alpha-1D chain
TD: Tubulin beta-4B chain
TE: Tubulin alpha-1D chain
TF: Tubulin beta-4B chain
TG: Tubulin alpha-1D chain
TH: Tubulin beta-4B chain
TI: Tubulin alpha-1D chain
TJ: Tubulin beta-4B chain
TK: Tubulin alpha-1D chain
TL: Tubulin beta-4B chain
TM: Tubulin alpha-1D chain
UC: Tubulin alpha-1D chain
UD: Tubulin beta-4B chain
UE: Tubulin alpha-1D chain
UF: Tubulin beta-4B chain
UG: Tubulin alpha-1D chain
UH: Tubulin beta-4B chain
UI: Tubulin alpha-1D chain
UJ: Tubulin beta-4B chain
UK: Tubulin alpha-1D chain
UL: Tubulin beta-4B chain
UM: Tubulin alpha-1D chain
VC: Tubulin alpha-1D chain
VD: Tubulin beta-4B chain
VE: Tubulin alpha-1D chain
VF: Tubulin beta-4B chain
VG: Tubulin alpha-1D chain
VH: Tubulin beta-4B chain
VI: Tubulin alpha-1D chain
VJ: Tubulin beta-4B chain
VK: Tubulin alpha-1D chain
VL: Tubulin beta-4B chain
VM: Tubulin alpha-1D chain
WC: Tubulin alpha-1D chain
WD: Tubulin beta-4B chain
WE: Tubulin alpha-1D chain
WF: Tubulin beta-4B chain
WG: Tubulin alpha-1D chain
WH: Tubulin beta-4B chain
WI: Tubulin alpha-1D chain
WJ: Tubulin beta-4B chain
WK: Tubulin alpha-1D chain
WL: Tubulin beta-4B chain
WM: Tubulin alpha-1D chain
WN: Tubulin beta-4B chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,409,018765
ポリマ－19,278,719395
非ポリマー130,299370
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 , 29種, 357分子 1A1K1L1N1O1P1R2F2G2H2S2T3A3C3D3F3H3N3O3P3Q3S3T3U3V3X3Y3Z4A4B...

#1: タンパク質 Armadillo repeat containing 4


分子量: 116017.070 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1B8W3
#4: タンパク質 Uncharacterized protein C1orf158 homolog


分子量: 23271.453 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2TA11
#5: タンパク質 Protein Flattop / Cilia- and flagella-associated protein 126


分子量: 21214.035 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q3SZT6
#6: タンパク質 CFAP141


分子量: 12361.437 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32L75
#10: タンパク質 CFAP276


分子量: 19387.805 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1B9I5
#13: タンパク質 Methyl-CpG binding domain protein 1


分子量: 62138.992 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: F1N7G5
#15: タンパク質 CFAP95


分子量: 26661.025 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32L77
#16: タンパク質 Cilia-and flagella-associated protein 96


分子量: 34554.371 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: F1N3A8
#17: タンパク質 EF-hand calcium-binding domain-containing protein 1 / Calaxin


分子量: 24667.131 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32L26
#18: タンパク質 EF-hand calcium binding domain 6


分子量: 162942.844 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A0AAA9SGY2
#20: タンパク質
EFHC2


分子量: 85566.766 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A0A3Q1N1R0
#21: タンパク質
Enkurin, TRPC channel interacting protein


分子量: 30215.129 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1B836
#22: タンパク質
Protein FAM166B


分子量: 30551.627 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2TBR5
#24: タンパク質 Meiosis-specific nuclear structural protein 1


分子量: 60538.367 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2KIQ2
#25: タンパク質 Nucleoside diphosphate kinase 7 / NDK 7 / NDP kinase 7


分子量: 42650.895 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q5E9Y9, nucleoside-diphosphate kinase
#26: タンパク質 Outer dynein arm-docking complex subunit 3 / Coiled-coil domain-containing protein 151


分子量: 72163.984 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A7MBH5
#27: タンパク質
PACRG protein / Parkin coregulated


分子量: 29323.059 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A5PK71
#28: タンパク質 Pierce1


分子量: 15673.458 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32P67
#29: タンパク質 Pierce2


分子量: 13784.531 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A0A3Q1LFK7
#30: タンパク質 RIB43A-like with coiled-coils protein 2


分子量: 44773.418 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32LJ7
#31: タンパク質
Sperm acrosome associated 9


分子量: 19345.191 Da / 分子数: 7 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A0A3Q1MYU9
#32: タンパク質
Tektin-1


分子量: 48798.375 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32KZ9
#33: タンパク質
Tektin-2


分子量: 49962.656 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2T9Q6
#34: タンパク質
Tektin-3


分子量: 56760.910 Da / 分子数: 14 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A6H782
#35: タンパク質
Tektin-4


分子量: 52025.488 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2TA38
#36: タンパク質 TTC25 protein / Tetratricopeptide repeat domain 25


分子量: 78492.633 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A5PK42
#40: タンパク質 Sperm associated antigen 8


分子量: 51604.398 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1BNS6
#41: タンパク質 ...
Tubulin beta-4B chain / Tubulin beta-2C chain


分子量: 49877.824 Da / 分子数: 130 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q3MHM5
#42: タンパク質 ...
Tubulin alpha-1D chain


分子量: 50335.594 Da / 分子数: 134 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2HJ86

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Coiled-coil domain containing ... , 2種, 5分子 1D1E1F1H1I

#2: タンパク質 Coiled-coil domain containing 114


分子量: 77675.969 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: F1N2N9
#3: タンパク質 Coiled-coil domain containing 173


分子量: 65437.598 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1BJL9

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Cilia and flagella associated protein ... , 5種, 15分子 1T1U2J2K2L2M2O2P2Q2V2W2X2Y7K7L

#7: タンパク質 Cilia and flagella associated protein 161 / CFAP161


分子量: 36519.594 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: F6RJC2
#11: タンパク質
Cilia and flagella associated protein 45 / Coiled-coil domain containing 19


分子量: 65800.328 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32LN4
#12: タンパク質 Cilia and flagella associated protein 52


分子量: 68719.602 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1BKF9
#14: タンパク質
Cilia and flagella associated protein 77


分子量: 32999.203 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A0A3Q1LJD6
#39: タンパク質 Cilia and flagella associated protein 90


分子量: 16820.848 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A0A3Q1LU45

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Cilia- and flagella-associated protein ... , 2種, 7分子 1W1X1Y1Z2A2B4D

#8: タンパク質
Cilia- and flagella-associated protein 20


分子量: 22781.389 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q6B857
#23: タンパク質 Cilia- and flagella-associated protein 144 / Protein FAM183A


分子量: 16178.324 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A8QW39

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EF-hand domain ... , 2種, 5分子 2D2E3J3K3L

#9: タンパク質 EF-hand domain family member B


分子量: 97960.547 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: F1MMV1
#19: タンパク質 EF-hand domain containing 1


分子量: 74125.344 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1BKH1

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Ciliary microtubule associated protein ... , 2種, 6分子 7C7D7E7F7H7I

#37: タンパク質
Ciliary microtubule associated protein 1A


分子量: 27684.936 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
#38: タンパク質 Ciliary microtubule associated protein 1C


分子量: 30860.854 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A0A452DIY7

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非ポリマー , 3種, 370分子

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


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 130 / 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
#44: 化合物...
ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 106 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#45: 化合物...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


分子量: 523.180 Da / 分子数: 134 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: GTP, 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 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: 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: bovine fallopian tube cilia / タイプ: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#42 / 由来: NATURAL
分子量実験値: NO
由来(天然)生物種: Bos taurus (ウシ)
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: 3.52 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 153589 / 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

他の情報も見る