+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14730 | |||||||||
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Title | Tomogram of chicken sperm distal microtubules | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Microtubule Sperm / UNKNOWN FUNCTION | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Hoog JL / Croft JT / Zabeo DZ | |||||||||
Funding support | Sweden, 2 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14730.map.gz | 2 GB | EMDB map data format | |
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Header (meta data) | emd-14730-v30.xml emd-14730.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | emd_14730.png | 95 KB | ||
Filedesc metadata | emd-14730.cif.gz | 3.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14730 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14730 | HTTPS FTP |
-Validation report
Summary document | emd_14730_validation.pdf.gz | 483.1 KB | Display | EMDB validaton report |
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Full document | emd_14730_full_validation.pdf.gz | 482.6 KB | Display | |
Data in XML | emd_14730_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | emd_14730_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14730 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14730 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14730.map.gz / Format: CCP4 / Size: 2.5 GB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||
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Voxel size | X=Y=Z: 4.37 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Chicken sperm flagellum end piece
Entire | Name: Chicken sperm flagellum end piece |
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Components |
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-Supramolecule #1: Chicken sperm flagellum end piece
Supramolecule | Name: Chicken sperm flagellum end piece / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Gallus gallus (chicken) / Tissue: Sperm / Organelle: Flagellum / Location in cell: End piece |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
Details | Sample directly applied to a glow-discharged EM grid after collection. |
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-5 / Average exposure time: 3.0 sec. / Average electron dose: 1.344 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 33000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Software - Name: IMOD / Number images used: 61 |
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