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- PDB-6ody: Cryo-EM structure of Helicobacter pylori VacA hexamer -

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Basic information

Entry
Database: PDB / ID: 6ody
TitleCryo-EM structure of Helicobacter pylori VacA hexamer
ComponentsVacuolating cytotoxin autotransporter
KeywordsTOXIN / VacA
Function / homology
Function and homology information


cell outer membrane / toxin activity / periplasmic space / cell surface / extracellular region
Similarity search - Function
Vacuolating cytotoxin / Vacuolating cyotoxin / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily
Similarity search - Domain/homology
Vacuolating cytotoxin autotransporter
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsErwin, A.L. / Cover, T.L. / Ohi, M.D.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI039657 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA116087 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM08230 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118089 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)T32CA119925 United States
Other government5I01BX000627 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31AI112324 United States
CitationJournal: 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
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: Vacuolating cytotoxin autotransporter
B: Vacuolating cytotoxin autotransporter
C: Vacuolating cytotoxin autotransporter
D: Vacuolating cytotoxin autotransporter
E: Vacuolating cytotoxin autotransporter
F: Vacuolating cytotoxin autotransporter


Theoretical massNumber of molelcules
Total (without water)422,3556
Polymers422,3556
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4960 Å2
ΔGint-31 kcal/mol
Surface area182800 Å2

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Components

#1: Protein
Vacuolating cytotoxin autotransporter


Mass: 70392.578 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Helicobacter pylori (bacteria) / Variant: strep tag 808 / Strain: s1/i1/m1 / References: UniProt: Q48245

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vacuolating cytotoxin A / Type: COMPLEX / Details: Hexamer / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.528 MDa / Experimental value: YES
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: s1/i1/m1
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133827 / Symmetry type: POINT

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