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- EMDB-13877: subtomogram average of paracrystalline patches from the acrosome ... -

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Basic information

Entry
Database: EMDB / ID: EMD-13877
Titlesubtomogram average of paracrystalline patches from the acrosome of capacitated boar sperm
Map datasubtomogram average of paracrystalline patches in the acrosome of capacitated boar sperm
Sample
  • Organelle or cellular component: paracrystalline patches of unknown composition found in the acrosome of boar sperm
Biological speciesSus scrofa (pig)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsLeung MR / Zeev-Ben-Mordehai T
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)740.018.007 Netherlands
CitationJournal: 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
DepositionNov 15, 2021-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateSep 21, 2022-
Current statusSep 21, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_13877.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram average of paracrystalline patches in the acrosome of capacitated boar sperm
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.44 Å/pix.
x 160 pix.
= 869.76 Å
5.44 Å/pix.
x 160 pix.
= 869.76 Å
5.44 Å/pix.
x 160 pix.
= 869.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.436 Å
Density
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-4.029724 - 5.1099243
Average (Standard dev.)-0.024854362 (±0.8644224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 869.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : paracrystalline patches of unknown composition found in the acros...

EntireName: paracrystalline patches of unknown composition found in the acrosome of boar sperm
Components
  • Organelle or cellular component: paracrystalline patches of unknown composition found in the acrosome of boar sperm

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Supramolecule #1: paracrystalline patches of unknown composition found in the acros...

SupramoleculeName: paracrystalline patches of unknown composition found in the acrosome of boar sperm
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig) / Tissue: sperm / Organelle: acrosome / Location in cell: acrosomal matrix

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 7.6
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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

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Image processing

ExtractionNumber tomograms: 2 / Number images used: 2168 / Reference model: random particle from dataset
CTF correctionSoftware - Name: IMOD (ver. 4.10.25)
Final angle assignmentType: OTHER / Software - Name: PEET
Final reconstructionNumber 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

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