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- EMDB-17467: Subtomogram representing a segment of the outer wall of empty ger... -

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Basic information

Entry
Database: EMDB / ID: EMD-17467
TitleSubtomogram representing a segment of the outer wall of empty germinated polar tubes from Vairimorpha necatrix.
Map dataMerged map after refinement.
Sample
  • Organelle or cellular component: Subtomogram representing a segment of the outer wall of cargo-filled, germinated polar tubes from Vairimorpha necatrix.
KeywordsPolar tube / Subtomogram / Microsporidia / CELL INVASION
Biological speciesVairimorpha necatrix (fungus)
Methodsubtomogram averaging / cryo EM / Resolution: 25.7 Å
AuthorsSharma H / Ehrenbolger K / Jespersen N / Carlson LA / Barandun J
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)948655European Union
European Commission101033469European Union
CitationJournal: Biorxiv / Year: 2023
Title: Ribosome clustering and surface layer reorganization in the microsporidian host-invasion apparatus
Authors: Sharma H / Jespersen N / Ehrenbolger K / Carlson LA / Barandun J
History
DepositionMay 27, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17467.png

Downloads & links

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Map

FileDownload / File: emd_17467.map.gz / Format: CCP4 / Size: 128.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMerged map after refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.69 Å/pix.
x 32 pix.
= 278.08 Å		8.69 Å/pix.
x 32 pix.
= 278.08 Å		8.69 Å/pix.
x 32 pix.
= 278.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-3.2923517 - 3.8827245
Average (Standard dev.)-0.023148216 (±0.7687313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-16-16-16
Dimensions323232
Spacing323232
CellA=B=C: 278.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17467_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from refinement.

Fileemd_17467_half_map_1.map
AnnotationHalf map 1 from refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from refinement.

Fileemd_17467_half_map_2.map
AnnotationHalf map 1 from refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Subtomogram representing a segment of the outer wall of cargo-fil...

EntireName: Subtomogram representing a segment of the outer wall of cargo-filled, germinated polar tubes from Vairimorpha necatrix.
Components
  • Organelle or cellular component: Subtomogram representing a segment of the outer wall of cargo-filled, germinated polar tubes from Vairimorpha necatrix.

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Supramolecule #1: Subtomogram representing a segment of the outer wall of cargo-fil...

SupramoleculeName: Subtomogram representing a segment of the outer wall of cargo-filled, germinated polar tubes from Vairimorpha necatrix.
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Vairimorpha necatrix (fungus) / Organ: Polar tube / Location in cell: spores

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
1.0 mMC4H11NO3Tris-HCl
0.17 mMKClPotassium Chloride
10.0 mMC10H16N2O8EDTA

Details: Germination buffer (0.17 mM KCl, 1 mM Tris-HCl (pH 8.0), 10 mM EDTA)
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsSubtomogram representing a segment of the outer wall of cargo-filled, germinated polar tubes from Vairimorpha nectrix.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 1.0 sec. / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 25.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.91) / Number subtomograms used: 1479
ExtractionNumber tomograms: 21 / Number images used: 19576
Reference model: Generated by averaging manually picked particles
Software - Name: Dynamo (ver. 1.1.532)
Details: Particles were picked manually combined with surface models in the Dynamo package.
Final 3D classificationNumber classes: 2 / Avg.num./class: 1479 / Software - Name: Dynamo (ver. 1.1.532)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: Dynamo (ver. 1.1.532)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER

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