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- EMDB-28231: Subtomogram averages of the pre-conoid ring P1 and P2 from the cr... -

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Basic information

Entry
Database: EMDB / ID: EMD-28231
TitleSubtomogram averages of the pre-conoid ring P1 and P2 from the cryo-FIB milled Neospora caninum
Map data20-angstrom low-pass filtered EM map
Sample
  • Cell: The cryo-FIB milled lamella from Neospora caninum in both protruded and retracted states
Biological speciesNeospora caninum (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 49.0 Å
AuthorsGui L / O'Shaughnessy WJ / Cai K / Reetz E / Reese ML / Nicastro D
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM083122 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150715 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP140082 United States
National Science Foundation (NSF, United States)MCB1553334 United States
Welch FoundationI-2075-20210327 United States
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-tomography reveals rigid-body motion and organization of apicomplexan invasion machinery.
Authors: Long Gui / William J O'Shaughnessy / Kai Cai / Evan Reetz / Michael L Reese / Daniela Nicastro /
Abstract: The apical complex is a specialized collection of cytoskeletal and secretory machinery in apicomplexan parasites, which include the pathogens that cause malaria and toxoplasmosis. Its structure and ...The apical complex is a specialized collection of cytoskeletal and secretory machinery in apicomplexan parasites, which include the pathogens that cause malaria and toxoplasmosis. Its structure and mechanism of motion are poorly understood. We used cryo-FIB-milling and cryo-electron tomography to visualize the 3D-structure of the apical complex in its protruded and retracted states. Averages of conoid-fibers revealed their polarity and unusual nine-protofilament arrangement with associated proteins connecting and likely stabilizing the fibers. Neither the structure of the conoid-fibers nor the architecture of the spiral-shaped conoid complex change during protrusion or retraction. Thus, the conoid moves as a rigid body, and is not spring-like and compressible, as previously suggested. Instead, the apical-polar-rings (APR), previously considered rigid, dilate during conoid protrusion. We identified actin-like filaments connecting the conoid and APR during protrusion, suggesting a role during conoid movements. Furthermore, our data capture the parasites in the act of secretion during conoid protrusion.
History
DepositionSep 26, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28231.png

Downloads & links

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Map

FileDownload / File: emd_28231.map.gz / Format: CCP4 / Size: 45.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation20-angstrom low-pass filtered EM map
Voxel sizeX=Y=Z: 3.151 Å
Density
Contour LevelBy AUTHOR: 126.7
Minimum - Maximum119.92621 - 130.62006
Average (Standard dev.)124.98547 (±1.0374485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-50
Dimensions200200300
Spacing200200300
CellA: 630.2 Å / B: 630.2 Å / C: 945.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Original EM map, no filter is applied

Fileemd_28231_additional_1.map
AnnotationOriginal EM map, no filter is applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28231_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28231_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The cryo-FIB milled lamella from Neospora caninum in both protrud...

EntireName: The cryo-FIB milled lamella from Neospora caninum in both protruded and retracted states
Components
  • Cell: The cryo-FIB milled lamella from Neospora caninum in both protruded and retracted states

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Supramolecule #1: The cryo-FIB milled lamella from Neospora caninum in both protrud...

SupramoleculeName: The cryo-FIB milled lamella from Neospora caninum in both protruded and retracted states
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Neospora caninum (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 49.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 180
ExtractionNumber tomograms: 4 / Number images used: 180
Final angle assignmentType: NOT APPLICABLE

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