+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25673 | |||||||||||||||||||||
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Title | Prepore structure of pore-forming toxin Epx1 | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Keywords | pore-forming toxin / TOXIN | |||||||||||||||||||||
Biological species | Enterococcus faecalis (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||||||||||||||
Authors | Xiong XZ / Yang P | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25673.map.gz | 46.5 MB | EMDB map data format | |
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Header (meta data) | emd-25673-v30.xml emd-25673.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_25673.png | 52.6 KB | ||
Filedesc metadata | emd-25673.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25673 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25673 | HTTPS FTP |
-Validation report
Summary document | emd_25673_validation.pdf.gz | 422.1 KB | Display | EMDB validaton report |
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Full document | emd_25673_full_validation.pdf.gz | 421.7 KB | Display | |
Data in XML | emd_25673_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_25673_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25673 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25673 | HTTPS FTP |
-Related structure data
Related structure data | 7t4eMC 7t4dC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25673.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Epx1
Entire | Name: Epx1 |
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Components |
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-Supramolecule #1: Epx1
Supramolecule | Name: Epx1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Enterococcus faecalis (bacteria) |
-Macromolecule #1: Epx1
Macromolecule | Name: Epx1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Enterococcus faecalis (bacteria) |
Molecular weight | Theoretical: 37.01727 KDa |
Recombinant expression | Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.07 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119503 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |