[English] 日本語
Yorodumi
- PDB-9cpb: Atomic model of bovine Fallopian tube cilia doublet microtubule (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cpb
TitleAtomic model of bovine Fallopian tube cilia doublet microtubule (48-nm periodicity)
Components
  • (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
KeywordsSTRUCTURAL PROTEIN / axoneme / cilia / microtubule / dynein / Fallopian tube / doublet microtubule (DMT)
Function / homology
Function and homology information


outer dynein arm docking complex / regulation of cilium movement / mucociliary clearance / 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 / protein localization to motile cilium / sperm flagellum assembly ...outer dynein arm docking complex / regulation of cilium movement / mucociliary clearance / 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 / protein localization to motile cilium / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / manchette / regulation of flagellated sperm motility / protein polyglutamylation / inner dynein arm assembly / regulation of calcineurin-NFAT signaling cascade / positive regulation of feeding behavior / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cilium-dependent cell motility / outer dynein arm assembly / COPI-dependent Golgi-to-ER retrograde traffic / 9+0 non-motile cilium / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases activate IQGAPs / cerebrospinal fluid circulation / sperm principal piece / regulation of cilium beat frequency involved in ciliary motility / RHO GTPases Activate Formins / cilium movement involved in cell motility / regulation of store-operated calcium entry / Transferases; Transferring phosphorus-containing groups / 9+2 motile cilium / MHC class II antigen presentation / acrosomal membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / regulation of cilium assembly / ciliary transition zone / cilium movement / axoneme assembly / Aggrephagy / calcium ion sensor activity / The role of GTSE1 in G2/M progression after G2 checkpoint / axonemal microtubule / Separation of Sister Chromatids / cilium organization / ciliary tip / 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 / Recruitment of NuMA to mitotic centrosomes / gamma-tubulin ring complex / flagellated sperm motility / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / UTP biosynthetic process / CTP biosynthetic process / determination of left/right symmetry / Neutrophil degranulation / motile cilium / nucleoside diphosphate kinase activity / ciliary rootlet / GTP biosynthetic process / positive regulation of cell motility / AMP binding / regulation of neuron projection development / ciliary base / beta-tubulin binding / spermatid development / cerebral cortex cell migration / microtubule organizing center / regulation of cell division / mitotic cytokinesis / sperm flagellum / cellular response to UV-C / axoneme / cilium assembly / glial cell projection / single fertilization / alpha-tubulin binding / regulation of signal transduction / intercellular bridge / cytoplasmic microtubule / 3'-5' exonuclease activity / sperm midpiece / centriole / Hsp70 protein binding / acrosomal vesicle
Similarity search - Function
Outer dynein arm-docking complex subunit 4 / : / Protein of unknown function DUF4541 / Cilia and flagella associated protein 90 / DJBP, EF-hand domain / Protein of unknown function DUF4586 / Outer dynein arm-docking complex subunit 3 / EF-hand domain / Cilia-and flagella-associated protein 96 / Sperm-tail PG-rich repeat ...Outer dynein arm-docking complex subunit 4 / : / Protein of unknown function DUF4541 / Cilia and flagella associated protein 90 / DJBP, EF-hand domain / Protein of unknown function DUF4586 / Outer dynein arm-docking complex subunit 3 / EF-hand domain / Cilia-and flagella-associated protein 96 / Sperm-tail PG-rich repeat / FAM183 family / Sperm-tail PG-rich repeat / 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 161-like domain / 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 / Recoverin family / Parkin co-regulated protein / Parkin co-regulated protein / EF hand / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase / 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 / Tubulin-beta mRNA autoregulation signal. / TPR repeat region circular profile. / 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. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tetratricopeptide repeats / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain
Similarity search - Domain/homology
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 homolog 7 / Cilia- and flagella-associated protein 20
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsSun, C. / Zeng, J. / Zhang, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM138854 United States
CitationJournal: Nature / Year: 2025
Title: Structural diversity of axonemes across mammalian motile cilia.
Authors: 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 /
Abstract: 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.
History
DepositionJul 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Feb 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.3Mar 19, 2025Group: Data collection / Structure summary / Category: audit_author / em_admin / Item: _audit_author.name / _em_admin.last_update
Revision 1.1Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,409,018765
Polymers19,278,719395
Non-polymers130,299370
Water00
1


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

-
Components

+
Protein , 29 types, 357 molecules 1A1K1L1N1O1P1R2F2G2H2S2T3A3C3D3F3H3N3O3P3Q3S3T3U3V3X3Y3Z4A4B...

#1: Protein Armadillo repeat containing 4


Mass: 116017.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: E1B8W3
#4: Protein Uncharacterized protein C1orf158 homolog


Mass: 23271.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2TA11
#5: Protein Protein Flattop / Cilia- and flagella-associated protein 126


Mass: 21214.035 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3SZT6
#6: Protein CFAP141


Mass: 12361.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32L75
#10: Protein CFAP276


Mass: 19387.805 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: E1B9I5
#13: Protein Methyl-CpG binding domain protein 1


Mass: 62138.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: F1N7G5
#15: Protein CFAP95


Mass: 26661.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32L77
#16: Protein Cilia-and flagella-associated protein 96


Mass: 34554.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: F1N3A8
#17: Protein EF-hand calcium-binding domain-containing protein 1 / Calaxin


Mass: 24667.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32L26
#18: Protein EF-hand calcium binding domain 6


Mass: 162942.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A0AAA9SGY2
#20: Protein
EFHC2


Mass: 85566.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A0A3Q1N1R0
#21: Protein
Enkurin, TRPC channel interacting protein


Mass: 30215.129 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: E1B836
#22: Protein
Protein FAM166B


Mass: 30551.627 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2TBR5
#24: Protein Meiosis-specific nuclear structural protein 1


Mass: 60538.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2KIQ2
#25: Protein Nucleoside diphosphate kinase 7 / NDK 7 / NDP kinase 7


Mass: 42650.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q5E9Y9, nucleoside-diphosphate kinase
#26: Protein Outer dynein arm-docking complex subunit 3 / Coiled-coil domain-containing protein 151


Mass: 72163.984 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A7MBH5
#27: Protein
PACRG protein / Parkin coregulated


Mass: 29323.059 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A5PK71
#28: Protein Pierce1


Mass: 15673.458 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32P67
#29: Protein Pierce2


Mass: 13784.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A0A3Q1LFK7
#30: Protein RIB43A-like with coiled-coils protein 2


Mass: 44773.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32LJ7
#31: Protein
Sperm acrosome associated 9


Mass: 19345.191 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A0A3Q1MYU9
#32: Protein
Tektin-1


Mass: 48798.375 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32KZ9
#33: Protein
Tektin-2


Mass: 49962.656 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2T9Q6
#34: Protein
Tektin-3


Mass: 56760.910 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A6H782
#35: Protein
Tektin-4


Mass: 52025.488 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2TA38
#36: Protein TTC25 protein / Tetratricopeptide repeat domain 25


Mass: 78492.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A5PK42
#40: Protein Sperm associated antigen 8


Mass: 51604.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: E1BNS6
#41: Protein ...
Tubulin beta-4B chain / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3MHM5
#42: Protein ...
Tubulin alpha-1D chain


Mass: 50335.594 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2HJ86

-
Coiled-coil domain containing ... , 2 types, 5 molecules 1D1E1F1H1I

#2: Protein Coiled-coil domain containing 114


Mass: 77675.969 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: F1N2N9
#3: Protein Coiled-coil domain containing 173


Mass: 65437.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: E1BJL9

-
Cilia and flagella associated protein ... , 5 types, 15 molecules 1T1U2J2K2L2M2O2P2Q2V2W2X2Y7K7L

#7: Protein Cilia and flagella associated protein 161 / CFAP161


Mass: 36519.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: F6RJC2
#11: Protein
Cilia and flagella associated protein 45 / Coiled-coil domain containing 19


Mass: 65800.328 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q32LN4
#12: Protein Cilia and flagella associated protein 52


Mass: 68719.602 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: E1BKF9
#14: Protein
Cilia and flagella associated protein 77


Mass: 32999.203 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A0A3Q1LJD6
#39: Protein Cilia and flagella associated protein 90


Mass: 16820.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A0A3Q1LU45

-
Cilia- and flagella-associated protein ... , 2 types, 7 molecules 1W1X1Y1Z2A2B4D

#8: Protein
Cilia- and flagella-associated protein 20


Mass: 22781.389 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B857
#23: Protein Cilia- and flagella-associated protein 144 / Protein FAM183A


Mass: 16178.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A8QW39

-
EF-hand domain ... , 2 types, 5 molecules 2D2E3J3K3L

#9: Protein EF-hand domain family member B


Mass: 97960.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: F1MMV1
#19: Protein EF-hand domain containing 1


Mass: 74125.344 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: E1BKH1

-
Ciliary microtubule associated protein ... , 2 types, 6 molecules 7C7D7E7F7H7I

#37: Protein
Ciliary microtubule associated protein 1A


Mass: 27684.936 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#38: Protein Ciliary microtubule associated protein 1C


Mass: 30860.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A0A452DIY7

-
Non-polymers , 3 types, 370 molecules

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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 130 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#44: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 106 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#45: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 134 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: bovine fallopian tube cilia / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#42 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153589 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

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

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more