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- EMDB-42087: Representative tomogram of Enterococcus faecium SagA deletion strain -

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Basic information

Entry
Database: EMDB / ID: EMD-42087
TitleRepresentative tomogram of Enterococcus faecium SagA deletion strain
Map dataRepresentative tomogram of Enterococcus faecium SagA deletion strain
Sample
  • Cell: Enterococcus faecium WT Com15
KeywordsBacteria / cancer therapy / HYDROLASE
Biological speciesEnterococcus faecium (bacteria)
Methodelectron tomography / cryo EM
AuthorsHang HC / Park D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA245292 United States
CitationJournal: bioRxiv / Year: 2024
Title: Secreted antigen A peptidoglycan hydrolase is essential for cell separation and priming of immune checkpoint inhibitor therapy.
Authors: Steven Klupt / Kyong Tkhe Fam / Xing Zhang / Pavan Kumar Chodisetti / Abeera Mehmood / Tumara Boyd / Danielle Grotjahn / Donghyun Park / Howard C Hang /
Abstract: is a microbiota species in humans that can modulate host immunity, but has also acquired antibiotic resistance and is a major cause of hospital-associated infections. Notably, diverse strains of ... is a microbiota species in humans that can modulate host immunity, but has also acquired antibiotic resistance and is a major cause of hospital-associated infections. Notably, diverse strains of produce SagA, a highly conserved peptidoglycan hydrolase that is sufficient to promote intestinal immunity and immune checkpoint inhibitor antitumor activity. However, the functions of SagA in were unknown. Here we report that deletion of impaired growth and resulted in bulged and clustered enterococci due to defective peptidoglycan cleavage and cell separation. Moreover, Δ showed increased antibiotic sensitivity, yielded lower levels of active muropeptides, displayed reduced activation of the peptidoglycan pattern-recognition receptor NOD2, and failed to promote cancer immunotherapy. Importantly, plasmid-based expression of SagA, but not its catalytically-inactive mutant, restored Δ growth, production of active muropeptides and NOD2 activation. SagA is therefore essential for growth, stress resistance and activation of host immunity.
History
DepositionSep 22, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42087.png

Downloads & links

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Map

FileDownload / File: emd_42087.map.gz / Format: CCP4 / Size: 175.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRepresentative tomogram of Enterococcus faecium SagA deletion strain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
21.1 Å/pix.
x 125 pix.
= 2637.5 Å		21.1 Å/pix.
x 720 pix.
= 15192. Å		21.1 Å/pix.
x 511 pix.
= 10782.101 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 21.1 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-13.019534999999999 - 2.4231353
Average (Standard dev.)-0.47763002 (±0.27255934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720511125
Spacing511720125
CellA: 10782.101 Å / B: 15192.0 Å / C: 2637.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Enterococcus faecium WT Com15

EntireName: Enterococcus faecium WT Com15
Components
  • Cell: Enterococcus faecium WT Com15

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Supramolecule #1: Enterococcus faecium WT Com15

SupramoleculeName: Enterococcus faecium WT Com15 / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Enterococcus faecium (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 10 / Focused ion beam - Duration: 30 / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 500 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 37

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