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Yorodumi- EMDB-13877: subtomogram average of paracrystalline patches from the acrosome ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13877 | |||||||||
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Title | subtomogram average of paracrystalline patches from the acrosome of capacitated boar sperm | |||||||||
Map data | subtomogram average of paracrystalline patches in the acrosome of capacitated boar sperm | |||||||||
Sample |
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Biological species | Sus scrofa (pig) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 35.0 Å | |||||||||
Authors | Leung MR / Zeev-Ben-Mordehai T | |||||||||
Funding support | Netherlands, 1 items
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Citation | Journal: Front Cell Dev Biol / Year: 2021 Title: Membrane Remodeling and Matrix Dispersal Intermediates During Mammalian Acrosomal Exocytosis. Authors: Miguel Ricardo Leung / Ravi Teja Ravi / Bart M Gadella / Tzviya Zeev-Ben-Mordehai / Abstract: To become fertilization-competent, mammalian sperm must undergo a complex series of biochemical and morphological changes in the female reproductive tract. These changes, collectively called ...To become fertilization-competent, mammalian sperm must undergo a complex series of biochemical and morphological changes in the female reproductive tract. These changes, collectively called capacitation, culminate in the exocytosis of the acrosome, a large vesicle overlying the nucleus. Acrosomal exocytosis is not an all-or-nothing event but rather a regulated process in which vesicle cargo disperses gradually. However, the structural mechanisms underlying this controlled release remain undefined. In addition, unlike other exocytotic events, fusing membranes are shed as vesicles; the cell thus loses the entire anterior two-thirds of its plasma membrane and yet remains intact, while the remaining nonvesiculated plasma membrane becomes fusogenic. Precisely how cell integrity is maintained throughout this drastic vesiculation process is unclear, as is how it ultimately leads to the acquisition of fusion competence. Here, we use cryoelectron tomography to visualize these processes in unfixed, unstained, fully hydrated sperm. We show that paracrystalline structures within the acrosome disassemble during capacitation and acrosomal exocytosis, representing a plausible mechanism for gradual dispersal of the acrosomal matrix. We find that the architecture of the sperm head supports an atypical membrane fission-fusion pathway that maintains cell integrity. Finally, we detail how the acrosome reaction transforms both the micron-scale topography and the nanoscale protein landscape of the sperm surface, thus priming the sperm for fertilization. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13877.map.gz | 10.6 MB | EMDB map data format | |
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Header (meta data) | emd-13877-v30.xml emd-13877.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_13877.png | 201.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13877 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13877 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13877.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | subtomogram average of paracrystalline patches in the acrosome of capacitated boar sperm | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.436 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : paracrystalline patches of unknown composition found in the acros...
Entire | Name: paracrystalline patches of unknown composition found in the acrosome of boar sperm |
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Components |
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-Supramolecule #1: paracrystalline patches of unknown composition found in the acros...
Supramolecule | Name: paracrystalline patches of unknown composition found in the acrosome of boar sperm type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Sus scrofa (pig) / Tissue: sperm / Organelle: acrosome / Location in cell: acrosomal matrix |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 2 / Number images used: 2168 / Reference model: random particle from dataset |
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CTF correction | Software - Name: IMOD (ver. 4.10.25) |
Final angle assignment | Type: OTHER / Software - Name: PEET |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.13.0) / Number subtomograms used: 1397 |