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- EMDB-72654: EsxX-EsxA-EsxB low resolution volume -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72654
TitleEsxX-EsxA-EsxB low resolution volume
Map datalow resolution volume for docking of AlphaFold complex
Sample
  • Complex: EsxX-EsxA-ESXB COMPLEX
KeywordsStaphylococcus aureus / immunity proteins / type VII secretion system / EsxX / EsxA / EsxB / IMMUNE SYSTEM
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsLea S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Cell Rep / Year: 2025
Title: Distinct immunity protein families mediate compartment-specific neutralization of a bacterial toxin.
Authors: Felicity Alcock / Yaping Yang / Justin Deme / Guillermina Casabona / Chriselle Mendonca / Fatima Ulhuq / Susan Lea / Tracy Palmer /
Abstract: Staphylococcus aureus utilizes a type VII secretion system (T7SS) to secrete antibacterial toxins targeting competitor bacteria. EsxX is a T7SS substrate protein harboring an N-terminal LXG domain, ...Staphylococcus aureus utilizes a type VII secretion system (T7SS) to secrete antibacterial toxins targeting competitor bacteria. EsxX is a T7SS substrate protein harboring an N-terminal LXG domain, which is secreted by ST398 strains. We demonstrate that the EsxX C terminus is a membrane-depolarizing toxin with a glycine zipper motif. EsxX is profoundly toxic to bacteria, displaying toxicity from both cytoplasmic and extracellular compartments. A pair of polytopic membrane proteins, ExiCD, protects cells from intoxication by extracellular EsxX. By contrast, a distinct soluble heterodimer, ExiAB, neutralizes cytoplasmic EsxX by sequestration of its glycine zipper motif in a binding groove on ExiB. exiA-exiB co-occur with esxX, consistent with protection from self-toxicity prior to EsxX secretion. By contrast, ExiCD is encoded by both EsxX producers and in antitoxin islands of competitor strains that do not encode EsxX, consistent with providing immunity against the secreted form of the toxin.
History
DepositionSep 10, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72654.png

Downloads & links

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Map

FileDownload / File: emd_72654.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlow resolution volume for docking of AlphaFold complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.46 Å/pix.
x 196 pix.
= 286.944 Å		1.46 Å/pix.
x 196 pix.
= 286.944 Å		1.46 Å/pix.
x 196 pix.
= 286.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.575
Minimum - Maximum-0.5185344 - 1.9244441
Average (Standard dev.)0.0007431417 (±0.0383543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 286.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_72654_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_72654_half_map_2.map
Annotationhalf 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 : EsxX-EsxA-ESXB COMPLEX

EntireName: EsxX-EsxA-ESXB COMPLEX
Components
  • Complex: EsxX-EsxA-ESXB COMPLEX

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Supramolecule #1: EsxX-EsxA-ESXB COMPLEX

SupramoleculeName: EsxX-EsxA-ESXB COMPLEX / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Staphylococcus aureus (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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Software - Name: cryoSPARC
Details: data are highly anisotropic - gold standard FSC gave resolution estimate of 3.7 but detail in volume suggests more reliably 6A
Number images used: 105726
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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