+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20024 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of Helicobacter pylori VacA hexamer | ||||||||||||||||||||||||
Map data | Cryo-EM structure of Helicobacter pylori VacA hexamer | ||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information cell outer membrane / toxin activity / periplasmic space / cell surface / extracellular region Similarity search - Function | ||||||||||||||||||||||||
Biological species | Helicobacter pylori (bacteria) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||||||||||||||
Authors | Erwin AL / Cover TL / Ohi MD | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: J Mol Biol / Year: 2019 Title: Cryo-EM Analysis Reveals Structural Basis of Helicobacter pylori VacA Toxin Oligomerization. Authors: Min Su / Amanda L Erwin / Anne M Campbell / Tasia M Pyburn / Lauren E Salay / Jessica L Hanks / D Borden Lacy / David L Akey / Timothy L Cover / Melanie D Ohi / Abstract: Helicobacter pylori colonizes the human stomach and contributes to the development of gastric cancer and peptic ulcer disease. H. pylori secretes a pore-forming toxin called vacuolating cytotoxin A ...Helicobacter pylori colonizes the human stomach and contributes to the development of gastric cancer and peptic ulcer disease. H. pylori secretes a pore-forming toxin called vacuolating cytotoxin A (VacA), which contains two domains (p33 and p55) and assembles into oligomeric structures. Using single-particle cryo-electron microscopy, we have determined low-resolution structures of a VacA dodecamer and heptamer, as well as a 3.8-Å structure of the VacA hexamer. These analyses show that VacA p88 consists predominantly of a right-handed beta-helix that extends from the p55 domain into the p33 domain. We map the regions of p33 and p55 involved in hexamer assembly, model how interactions between protomers support heptamer formation, and identify surfaces of VacA that likely contact membrane. This work provides structural insights into the process of VacA oligomerization and identifies regions of VacA protomers that are predicted to contact the host cell surface during channel formation. | ||||||||||||||||||||||||
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_20024.map.gz | 115.9 MB | EMDB map data format | |
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Header (meta data) | emd-20024-v30.xml emd-20024.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_20024.png | 37.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20024 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20024 | HTTPS FTP |
-Validation report
Summary document | emd_20024_validation.pdf.gz | 620.3 KB | Display | EMDB validaton report |
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Full document | emd_20024_full_validation.pdf.gz | 619.8 KB | Display | |
Data in XML | emd_20024_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_20024_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20024 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20024 | HTTPS FTP |
-Related structure data
Related structure data | 6odyMC 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_20024.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of Helicobacter pylori VacA hexamer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.25 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 : Vacuolating cytotoxin A
Entire | Name: Vacuolating cytotoxin A |
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Components |
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-Supramolecule #1: Vacuolating cytotoxin A
Supramolecule | Name: Vacuolating cytotoxin A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Hexamer |
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Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: s1/i1/m1 |
Molecular weight | Experimental: 528 KDa |
-Macromolecule #1: Vacuolating cytotoxin autotransporter
Macromolecule | Name: Vacuolating cytotoxin autotransporter / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: s1/i1/m1 |
Molecular weight | Theoretical: 70.392578 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)QPTQVID GPFAGGKDTV VNIDRINTKA DGTIKVGGFK ASLTTNAAHL NIGKGGVN L SNQASGRTLL VENLTGNITV DGPLRVNNQV GGYALAGSSA NFEFKAGVDT KNGTATFNND ISLGRFVNLK VDAHTANFK GIDTGNGGFN TLDFSGVTNK VNINKLITAS TNVAVKNFNI NELIVKTNGV SVGEYTHFSE DIGSQSRINT VRLETGTRSI FSGGVKFKS GEKLVIDEFY YSPWNYFDAR NIKNVEITRK FASSTPENPW GTSKLMFNNL TLGQNAVMDY SQFSNLTIQG D FINNQGTI NYLVRGGKVA TLNVGNAAAM MFNNDIDSAT GFYKPLIKIN SAQDLIKNTE HVLLKAKIIG YGNVSTGTNG IS NVNLEEQ FKERLALYNN NNRMDTCVVR NTDDIKACGM AIGNQSMVNN PDNYKYLIGK AWKNIGISKT ANGSKISVYY LGN STPTEN GGNTTNLPTN T |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Ab initio model |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133827 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: PROJECTION MATCHING |