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- EMDB-26624: Composite cryo-EM density map of the 48-nm repeat of the human re... -
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Open data
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Basic information
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Title | Composite cryo-EM density map of the 48-nm repeat of the human respiratory doublet microtubule | |||||||||||||||||||||
![]() | phenix auto-sharpened map | |||||||||||||||||||||
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![]() | cilia / microtubule / sperm / cell motility / STRUCTURAL PROTEIN | |||||||||||||||||||||
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 | |||||||||||||||||||||
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Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||
![]() | Gui M / Croft JT / Zabeo D / Acharya V / Kollman JM / Burgoyne T / Hoog JL / 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
Supplemental images |
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Downloads & links
-EMDB archive
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ungMC ![]() 7un1C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | phenix auto-sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Mask #1
+Additional map: local masked map
+Additional map: stitched unsharpened map
+Additional map: consensus refined map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: deepEMhancer sharpened map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Additional map: local masked map
+Half map: #2
+Half map: #1
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Sample components
+Entire : Doublet microtubule and associated proteins
+Supramolecule #1: Doublet microtubule and associated proteins
+Macromolecule #1: Protein CFAP95
+Macromolecule #2: EF-hand domain-containing family member B
+Macromolecule #3: Cilia- and flagella-associated protein 53
+Macromolecule #4: Nucleoside diphosphate kinase 7
+Macromolecule #5: Protein CFAP107
+Macromolecule #6: Protein CFAP141
+Macromolecule #7: Tektin-1
+Macromolecule #8: Tubulin alpha-1A chain
+Macromolecule #9: Tubulin beta-4B chain
+Macromolecule #10: Meiosis-specific nuclear structural protein 1
+Macromolecule #11: Tektin-2
+Macromolecule #12: Tektin-3
+Macromolecule #13: Sperm-associated antigen 8
+Macromolecule #14: Tektin-4
+Macromolecule #15: Cilia- and flagella-associated protein 161
+Macromolecule #16: Sperm acrosome-associated protein 9
+Macromolecule #17: Uncharacterized protein C15orf65
+Macromolecule #18: Protein FAM166B
+Macromolecule #19: UPF0686 protein C11orf1
+Macromolecule #20: Isoform 2 of Cilia- and flagella-associated protein 77
+Macromolecule #21: Protein FAM183A
+Macromolecule #22: Uncharacterized protein C5orf49
+Macromolecule #23: Protein FAM166C
+Macromolecule #24: RIB43A-like with coiled-coils protein 2
+Macromolecule #25: EF-hand domain-containing protein 1
+Macromolecule #26: EF-hand domain-containing family member C2
+Macromolecule #27: Cilia- and flagella-associated protein 20
+Macromolecule #28: Parkin coregulated gene protein
+Macromolecule #29: Cilia- and flagella-associated protein 45
+Macromolecule #30: Cilia- and flagella-associated protein 52
+Macromolecule #31: Enkurin
+Macromolecule #32: Protein Flattop
+Macromolecule #33: Protein CFAP210
+Macromolecule #34: Protein CFAP276
+Macromolecule #35: UPF0691 protein C9orf116
+Macromolecule #36: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.3 |
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Grid | Model: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |