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- EMDB-76880: Subtomogram averaging of vancomycin-resistant Enterococcus faeciu... -

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Basic information

Entry
Database: EMDB / ID: EMD-76880
TitleSubtomogram averaging of vancomycin-resistant Enterococcus faecium (delSagA-complemented)
Map data
Sample
  • Organelle or cellular component: Cell Wall
KeywordsEnterococcus faecium / Vancomycin / antibiotics / ANTIBIOTIC
Biological speciesEnterococcus faecium (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 26.0 Å
AuthorsPark D
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2026
Title: Genetic and pharmacological inactivation of peptidoglycan remodeling increases antibiotic susceptibility of vancomycin-resistant Enterococcus faecium.
Authors: Kyong T Fam / Pavan Kumar Chodisetti / Zifei Wang / Joshua A Homer / Christopher J Smedley / Seiya Kitamura / Benjamin Silva / Yijun Xiong / Althea Hansel-Harris / Matthew Holcomb / Simeon ...Authors: Kyong T Fam / Pavan Kumar Chodisetti / Zifei Wang / Joshua A Homer / Christopher J Smedley / Seiya Kitamura / Benjamin Silva / Yijun Xiong / Althea Hansel-Harris / Matthew Holcomb / Simeon Babarinde / Adrianna M Turner / Daria Van Tyne / Ian A Wilson / Stefano Forli / Benjamin F Cravatt / Donghyun Park / Dennis W Wolan / John E Moses / Howard C Hang /
Abstract: Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of healthcare-associated infections globally and demands new approaches for treatment. Here we show that genetic and ...Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of healthcare-associated infections globally and demands new approaches for treatment. Here we show that genetic and pharmacological inactivation of a highly conserved NlpC/P60 peptidoglycan hydrolase, secreted antigen A (SagA), enhanced vancomycin susceptibility of VREfm ex vivo and in vivo. Notably, genetic deletion of sagA impaired VREfm peptidoglycan remodeling, growth and increased the activity of vancomycin. We then identified first-in-class covalent NlpC/P60 peptidoglycan hydrolase inhibitors and demonstrated that pharmacological inactivation of SagA activity also impaired peptidoglycan remodeling and increased the efficacy of vancomycin across genetically distinct VREfm clinical isolates. Our study reveals peptidoglycan hydrolases are druggable targets whose inactivation improves the efficacy of vancomycin against VREfm.
History
DepositionApr 24, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76880.png

Downloads & links

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Map

FileDownload / File: emd_76880.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.55 Å/pix.
x 120 pix.
= 1266. Å		10.55 Å/pix.
x 120 pix.
= 1266. Å		10.55 Å/pix.
x 120 pix.
= 1266. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10.55 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.35
Minimum - Maximum-2.7406275 - 3.4976149
Average (Standard dev.)-0.00000020145434 (±1.1323786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 1266.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_76880_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76880_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 : Cell Wall

EntireName: Cell Wall
Components
  • Organelle or cellular component: Cell Wall

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Supramolecule #1: Cell Wall

SupramoleculeName: Cell Wall / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Enterococcus faecium (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS 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: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 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: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 2548
ExtractionNumber tomograms: 7 / Number images used: 2651 / Software - Name: Dynamo
CTF correctionType: NONE
Final angle assignmentType: NOT APPLICABLE

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