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Open data
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Basic information
Entry | Database: PDB / ID: 7ung | |||||||||||||||||||||
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Title | 48-nm repeat of the human respiratory doublet microtubule | |||||||||||||||||||||
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![]() | STRUCTURAL PROTEIN / cilia / microtubule / sperm / cell motility | |||||||||||||||||||||
Function / homology | ![]() 9+0 motile cilium / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / epithelial cilium movement involved in determination of left/right asymmetry / regulation of calcineurin-NFAT signaling cascade ...9+0 motile cilium / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / epithelial cilium movement involved in determination of left/right asymmetry / regulation of calcineurin-NFAT signaling cascade / inner dynein arm assembly / protein polyglutamylation / regulation of microtubule nucleation / positive regulation of feeding behavior / cerebrospinal fluid circulation / sperm axoneme assembly / cilium-dependent cell motility / sperm principal piece / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / regulation of store-operated calcium entry / 9+2 motile cilium / calcium ion sensor activity / Transferases; Transferring phosphorus-containing groups / acrosomal membrane / ciliary transition zone / cilium movement / Post-chaperonin tubulin folding pathway / axoneme assembly / axonemal microtubule / left/right axis specification / cilium organization / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / gamma-tubulin ring complex / Cilium Assembly / flagellated sperm motility / Carboxyterminal post-translational modifications of tubulin / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / neuron projection arborization / Intraflagellar transport / manchette / cytoskeleton-dependent intracellular transport / cerebellar cortex morphogenesis / Formation of tubulin folding intermediates by CCT/TriC / positive regulation of cilium assembly / Gap junction assembly / dentate gyrus development / COPI-independent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / CTP biosynthetic process / UTP biosynthetic process / Assembly and cell surface presentation of NMDA receptors / Kinesins / motile cilium / positive regulation of cell motility / determination of left/right symmetry / centrosome cycle / motor behavior / GTP biosynthetic process / COPI-dependent Golgi-to-ER retrograde traffic / microtubule organizing center / response to L-glutamate / intermediate filament / regulation of neuron projection development / ciliary base / smoothened signaling pathway / intercellular bridge / regulation of synapse organization / beta-tubulin binding / startle response / AMP binding / regulation of cell division / MHC class I protein binding / locomotory exploration behavior / cerebral cortex cell migration / Recycling pathway of L1 / microtubule polymerization / cytoplasmic microtubule / axoneme / microtubule-based process / centriolar satellite / spermatid development / mitotic cytokinesis / alpha-tubulin binding / cilium assembly / single fertilization / cellular response to UV-C / sperm flagellum / RHO GTPases activate IQGAPs / cellular response to unfolded protein / response to tumor necrosis factor / Hedgehog 'off' state / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / response to mechanical stimulus Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||
![]() | Gui, M. / Croft, J.T. / Zabeo, D. / Acharya, V. / Kollman, J.M. / Burgoyne, T. / Hoog, J.L. / Brown, A. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules. Authors: Miao Gui / Jacob T Croft / Davide Zabeo / Vajradhar Acharya / Justin M Kollman / Thomas Burgoyne / Johanna L Höög / Alan Brown / ![]() ![]() ![]() Abstract: The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins ...The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins (MIPs). Here, we used single-particle cryo-electron microscopy methods to build atomic models of two types of human ciliary microtubule: the doublet microtubules of multiciliated respiratory cells and the distal singlet microtubules of monoflagellated human spermatozoa. We discover that SPACA9 is a polyspecific MIP capable of binding both microtubule types. SPACA9 forms intralumenal striations in the B tubule of respiratory doublet microtubules and noncontinuous spirals in sperm singlet microtubules. By acquiring new and reanalyzing previous cryo-electron tomography data, we show that SPACA9-like intralumenal striations are common features of different microtubule types in animal cilia. Our structures provide detailed references to help rationalize ciliopathy-causing mutations and position cryo-EM as a tool for the analysis of samples obtained directly from ciliopathy patients. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 19.3 MB | Display | ![]() |
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Full document | ![]() | 19.8 MB | Display | |
Data in XML | ![]() | 3.3 MB | Display | |
Data in CIF | ![]() | 5.3 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26624MC ![]() 7un1C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
+Protein , 26 types, 408 molecules 075689AA0A1A2A3A4AAACAEAGAIAKAMBABCBEBGBIBKBMCACCCECG...
-EF-hand domain-containing family member ... , 2 types, 6 molecules 12WXYZ
#2: Protein | Mass: 93940.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #26: Protein | Mass: 87516.828 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Cilia- and flagella-associated protein ... , 5 types, 18 molecules 34EFXAXBXCXDXEXFXGabcdefg
#3: Protein | Mass: 61960.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | Mass: 34339.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #27: Protein | Mass: 22807.469 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) ![]() #29: Protein | Mass: 65858.109 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #30: Protein | Mass: 68379.062 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Uncharacterized protein ... , 2 types, 3 molecules GL1L2
#17: Protein | Mass: 13778.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#22: Protein | Mass: 17019.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 3 types, 451 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
#36: Chemical | ChemComp-GTP / #37: Chemical | ChemComp-MG / #38: Chemical | ChemComp-GDP / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Doublet microtubule and associated proteins / Type: COMPLEX / Entity ID: #1-#35 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.3 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R2/1 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208558 / Symmetry type: POINT |