+Open data
-Basic information
Entry | Database: PDB / ID: 7ung | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | 48-nm repeat of the human respiratory doublet microtubule | |||||||||||||||||||||
Components |
| |||||||||||||||||||||
Keywords | STRUCTURAL PROTEIN / cilia / microtubule / sperm / cell motility | |||||||||||||||||||||
Function / homology | Function and homology information 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 / regulation of calcineurin-NFAT signaling cascade / protein polyglutamylation / sperm axoneme assembly / inner dynein arm assembly / cilium-dependent cell motility ...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 / regulation of calcineurin-NFAT signaling cascade / protein polyglutamylation / sperm axoneme assembly / inner dynein arm assembly / cilium-dependent cell motility / regulation of microtubule nucleation / positive regulation of feeding behavior / cerebrospinal fluid circulation / regulation of cilium beat frequency involved in ciliary motility / sperm principal piece / cilium movement involved in cell motility / 9+2 motile cilium / regulation of store-operated calcium entry / cilium movement / Transferases; Transferring phosphorus-containing groups / calcium ion sensor activity / acrosomal membrane / axoneme assembly / Post-chaperonin tubulin folding pathway / flagellated sperm motility / cilium organization / axonemal microtubule / Carboxyterminal post-translational modifications of tubulin / left/right axis specification / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / gamma-tubulin ring complex / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / cytoskeleton-dependent intracellular transport / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / neuron projection arborization / manchette / Gap junction assembly / positive regulation of cilium assembly / Formation of tubulin folding intermediates by CCT/TriC / cerebellar cortex morphogenesis / 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 / UTP biosynthetic process / Kinesins / CTP biosynthetic process / Assembly and cell surface presentation of NMDA receptors / motile cilium / positive regulation of cell motility / determination of left/right symmetry / GTP biosynthetic process / centrosome cycle / intermediate filament / microtubule organizing center / motor behavior / COPI-dependent Golgi-to-ER retrograde traffic / response to L-glutamate / ciliary base / smoothened signaling pathway / regulation of synapse organization / intercellular bridge / beta-tubulin binding / regulation of neuron projection development / AMP binding / regulation of cell division / startle response / single fertilization / microtubule polymerization / Recycling pathway of L1 / axoneme / spermatid development / cerebral cortex cell migration / locomotory exploration behavior / mitotic cytokinesis / alpha-tubulin binding / cilium assembly / cellular response to UV-C / sperm flagellum / RHO GTPases activate IQGAPs / cellular response to unfolded protein / MHC class I protein binding / Hedgehog 'off' state / response to tumor necrosis factor / cytoplasmic microtubule / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / response to mechanical stimulus / Mitotic Prometaphase / homeostasis of number of cells within a tissue / EML4 and NUDC in mitotic spindle formation / condensed chromosome / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||
Authors | Gui, M. / Croft, J.T. / Zabeo, D. / Acharya, V. / Kollman, J.M. / Burgoyne, T. / Hoog, J.L. / Brown, A. | |||||||||||||||||||||
Funding support | United States, Sweden, 6items
| |||||||||||||||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ung.cif.gz | 26.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ung.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ung.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/7ung ftp://data.pdbj.org/pub/pdb/validation_reports/un/7ung | HTTPS FTP |
---|
-Related structure data
Related structure data | 26624MC 7un1C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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) Homo sapiens (human) / References: UniProt: Q8N7U6 #26: Protein | Mass: 87516.828 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5JST6 |
---|
-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) Homo sapiens (human) / References: UniProt: Q96M91 #15: Protein | Mass: 34339.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P656 #27: Protein | Mass: 22807.469 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6A4 #29: Protein | Mass: 65858.109 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UL16 #30: Protein | Mass: 68379.062 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N1V2 |
---|
-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) Homo sapiens (human) / References: UniProt: H3BRN8 |
---|---|
#22: Protein | Mass: 17019.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A4QMS7 |
-Non-polymers , 3 types, 451 molecules
#36: Chemical | ChemComp-GTP / #37: Chemical | ChemComp-MG / #38: Chemical | ChemComp-GDP / |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Doublet microtubule and associated proteins / Type: COMPLEX / Entity ID: #1-#35 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
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 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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) |
-Processing
EM software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |