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Yorodumi- EMDB-40620: cryo-EM density map of the 48-nm repeat doublet microtubule with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40620 | |||||||||
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Title | cryo-EM density map of the 48-nm repeat doublet microtubule with beak from Chlamydomonas | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Chlamydomonas / Tektin / beak / doublet microtubule / DMT / microtubule inner protein / cilia / flagella / FAP / CFAP / MIP / MAP / cytoskeleton / tublin / STRUCTURAL PROTEIN | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Zeng J / Zhang R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2023 Title: Structural specializations of the sperm tail. Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / ...Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / Tzviya Zeev-Ben-Mordehai / Abstract: Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule- ...Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule-based molecular machine-the axoneme-but it is unclear how axonemal microtubules are ornamented to support motility in diverse fertilization environments. Here, we present high-resolution structures of native axonemal doublet microtubules (DMTs) from sea urchin and bovine sperm, representing external and internal fertilizers. We identify >60 proteins decorating sperm DMTs; at least 15 are sperm associated and 16 are linked to infertility. By comparing DMTs across species and cell types, we define core microtubule inner proteins (MIPs) and analyze evolution of the tektin bundle. We identify conserved axonemal microtubule-associated proteins (MAPs) with unique tubulin-binding modes. Additionally, we identify a testis-specific serine/threonine kinase that links DMTs to outer dense fibers in mammalian sperm. Our study provides structural foundations for understanding sperm evolution, motility, and dysfunction at a molecular level. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40620.map.gz | 158.6 MB | EMDB map data format | |
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Header (meta data) | emd-40620-v30.xml emd-40620.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_40620.png | 156 KB | ||
Masks | emd_40620_msk_1.map | 512 MB | Mask map | |
Others | emd_40620_additional_1.map.gz emd_40620_half_map_1.map.gz emd_40620_half_map_2.map.gz | 480.1 MB 475 MB 475 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40620 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40620 | HTTPS FTP |
-Validation report
Summary document | emd_40620_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_40620_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_40620_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_40620_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40620 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40620 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40620.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40620_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_40620_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_40620_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40620_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chlamydomonas DMTs
Entire | Name: Chlamydomonas DMTs |
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Components |
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-Supramolecule #1: Chlamydomonas DMTs
Supramolecule | Name: Chlamydomonas DMTs / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 39.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102766 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |