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- EMDB-18524: Anti-feeding prophage with native Afp18 toxin -

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Basic information

Entry
Database: EMDB / ID: EMD-18524
TitleAnti-feeding prophage with native Afp18 toxin
Map dataAnti-feeding prophage with native Afp18 toxin
Sample
  • Complex: Anti-feeding prophage loaded with native Afp18 toxin
KeywordsContractile Injection System / CONTRACTILE PROTEIN
Biological speciesSerratia entomophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsRebrova EM / Taylor NMI
Funding support Denmark, 2 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
LundbeckfondenR346-2020-1683 Denmark
CitationJournal: Biorxiv / Year: 2023
Title: N-terminal toxin signal peptides efficiently load therapeutics into a natural nano-injection system
Authors: Steiner-Rebrova EM / Ejaz RN / Kielkopf CS / Ruiz MP / Marin-Arraiza L / Hendriks IA / Nissen JN / Pozdnyakova I / Pape T / Regaiolo A / Gotz K / Heermann R / Rasmussen S / Nielsen ML / Taylor NMI
History
DepositionSep 28, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18524.png

Downloads & links

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Map

FileDownload / File: emd_18524.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAnti-feeding prophage with native Afp18 toxin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 800 pix.
= 864. Å		1.08 Å/pix.
x 800 pix.
= 864. Å		1.08 Å/pix.
x 800 pix.
= 864. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8
Minimum - Maximum-2.7369568 - 4.906694
Average (Standard dev.)-0.00059806556 (±0.17048417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 864.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Anti-feeding prophage with native Afp18 toxin - Halp map A

Fileemd_18524_half_map_1.map
AnnotationAnti-feeding prophage with native Afp18 toxin - Halp map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Anti-feeding prophage with native Afp18 toxin - Halp map B

Fileemd_18524_half_map_2.map
AnnotationAnti-feeding prophage with native Afp18 toxin - Halp map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Anti-feeding prophage loaded with native Afp18 toxin

EntireName: Anti-feeding prophage loaded with native Afp18 toxin
Components
  • Complex: Anti-feeding prophage loaded with native Afp18 toxin

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Supramolecule #1: Anti-feeding prophage loaded with native Afp18 toxin

SupramoleculeName: Anti-feeding prophage loaded with native Afp18 toxin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Serratia entomophila (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 1xPBS
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: OTHER / Number real images: 8886 / Average exposure time: 0.57 sec. / Average electron dose: 39.83 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model was generated in CryoSPARC
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 49198
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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