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- EMDB-25673: Prepore structure of pore-forming toxin Epx1 -

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Basic information

Entry
Database: EMDB / ID: EMD-25673
TitlePrepore structure of pore-forming toxin Epx1
Map data
Sample
  • Complex: Epx1
    • Protein or peptide: Epx1
Keywordspore-forming toxin / TOXIN
Biological speciesEnterococcus faecalis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsXiong XZ / Yang P
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01NS080833 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01NS117626 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132387 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI139087 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI158503 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21NS106159 United States
CitationJournal: Cell / Year: 2022
Title: Emerging enterococcus pore-forming toxins with MHC/HLA-I as receptors.
Authors: Xiaozhe Xiong / Songhai Tian / Pan Yang / Francois Lebreton / Huan Bao / Kuanwei Sheng / Linxiang Yin / Pengsheng Chen / Jie Zhang / Wanshu Qi / Jianbin Ruan / Hao Wu / Hong Chen / David T ...Authors: Xiaozhe Xiong / Songhai Tian / Pan Yang / Francois Lebreton / Huan Bao / Kuanwei Sheng / Linxiang Yin / Pengsheng Chen / Jie Zhang / Wanshu Qi / Jianbin Ruan / Hao Wu / Hong Chen / David T Breault / Hao Wu / Ashlee M Earl / Michael S Gilmore / Jonathan Abraham / Min Dong /
Abstract: Enterococci are a part of human microbiota and a leading cause of multidrug resistant infections. Here, we identify a family of Enterococcus pore-forming toxins (Epxs) in E. faecalis, E. faecium, ...Enterococci are a part of human microbiota and a leading cause of multidrug resistant infections. Here, we identify a family of Enterococcus pore-forming toxins (Epxs) in E. faecalis, E. faecium, and E. hirae strains isolated across the globe. Structural studies reveal that Epxs form a branch of β-barrel pore-forming toxins with a β-barrel protrusion (designated the top domain) sitting atop the cap domain. Through a genome-wide CRISPR-Cas9 screen, we identify human leukocyte antigen class I (HLA-I) complex as a receptor for two members (Epx2 and Epx3), which preferentially recognize human HLA-I and homologous MHC-I of equine, bovine, and porcine, but not murine, origin. Interferon exposure, which stimulates MHC-I expression, sensitizes human cells and intestinal organoids to Epx2 and Epx3 toxicity. Co-culture with Epx2-harboring E. faecium damages human peripheral blood mononuclear cells and intestinal organoids, and this toxicity is neutralized by an Epx2 antibody, demonstrating the toxin-mediated virulence of Epx-carrying Enterococcus.
History
DepositionDec 9, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7t4e
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7t4e
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25673.png

Downloads & links

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Map

FileDownload / File: emd_25673.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 240 pix.
= 198. Å		0.83 Å/pix.
x 240 pix.
= 198. Å		0.83 Å/pix.
x 240 pix.
= 198. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.0017714028 - 1.669468
Average (Standard dev.)0.0052492134 (±0.052556142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 198.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8250.8250.825
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z198.000198.000198.000
α/β/γ90.00090.00090.000
start NX/NY/NZ138136120
NX/NY/NZ121111179
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0021.6690.005

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Supplemental data

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Sample components

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Entire : Epx1

EntireName: Epx1
Components
  • Complex: Epx1
    • Protein or peptide: Epx1

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Supramolecule #1: Epx1

SupramoleculeName: Epx1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Enterococcus faecalis (bacteria)

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Macromolecule #1: Epx1

MacromoleculeName: Epx1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis (bacteria)
Molecular weightTheoretical: 37.01727 KDa
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
SequenceString: DVQVFADNPV LGTEVTFEKD ENGRIVKIIS KNQYRITIYN SVDAGDTPND ASVSLDVDFI DDKNSGEMGA VASINTFIPS GLRYVEGYK YKGVTNPIYK NLSAGMLWPK KYRVEVVNIP IDQATKIITA TPNNNIKEKQ VSDTISYGFG GSVSADGKKP G GSIEANLA ...String:
DVQVFADNPV LGTEVTFEKD ENGRIVKIIS KNQYRITIYN SVDAGDTPND ASVSLDVDFI DDKNSGEMGA VASINTFIPS GLRYVEGYK YKGVTNPIYK NLSAGMLWPK KYRVEVVNIP IDQATKIITA TPNNNIKEKQ VSDTISYGFG GSVSADGKKP G GSIEANLA YTKTTTYDQP DYETSQIKKT TKEAVWDTSF VETRDGYTPN SWNPVYGNQM FMRGRYSNVS PIDNIKKGGE VS SLISGGF SPKMGVVLAS PNGTKKSQFV VRVSRMSDMY IMRWSGTEWG GENEINQNVP KEYNALMYED VKFEIDWEQR TVR TILEHH HHHH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.07 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119503
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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