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- PDB-6nyl: Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nyl | ||||||||||||
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Title | Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2c (OA-2c) | ||||||||||||
![]() | Vacuolating cytotoxin autotransporter | ||||||||||||
![]() | TOXIN / Helicobacter pylori / vacuolating cytotoxin A / pore-forming toxin | ||||||||||||
Function / homology | ![]() cell outer membrane / toxin activity / periplasmic space / cell surface / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
![]() | Zhang, K. / Zhang, H. / Li, S. / Au, S. / Chiu, W. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution. Authors: Kaiming Zhang / Huawei Zhang / Shanshan Li / Grigore D Pintilie / Tung-Chung Mou / Yuanzhu Gao / Qinfen Zhang / Henry van den Bedem / Michael F Schmid / Shannon Wing Ngor Au / Wah Chiu / ![]() ![]() Abstract: Human gastric pathogen () is the primary risk factor for gastric cancer and is one of the most prevalent carcinogenic infectious agents. Vacuolating cytotoxin A (VacA) is a key virulence factor ...Human gastric pathogen () is the primary risk factor for gastric cancer and is one of the most prevalent carcinogenic infectious agents. Vacuolating cytotoxin A (VacA) is a key virulence factor secreted by and induces multiple cellular responses. Although structural and functional studies of VacA have been extensively performed, the high-resolution structure of a full-length VacA protomer and the molecular basis of its oligomerization are still unknown. Here, we use cryoelectron microscopy to resolve 10 structures of VacA assemblies, including monolayer (hexamer and heptamer) and bilayer (dodecamer, tridecamer, and tetradecamer) oligomers. The models of the 88-kDa full-length VacA protomer derived from the near-atomic resolution maps are highly conserved among different oligomers and show a continuous right-handed β-helix made up of two domains with extensive domain-domain interactions. The specific interactions between adjacent protomers in the same layer stabilizing the oligomers are well resolved. For double-layer oligomers, we found short- and/or long-range hydrophobic interactions between protomers across the two layers. Our structures and other previous observations lead to a mechanistic model wherein VacA hexamer would correspond to the prepore-forming state, and the N-terminal region of VacA responsible for the membrane insertion would undergo a large conformational change to bring the hydrophobic transmembrane region to the center of the oligomer for the membrane channel formation. | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 871.9 KB | Display | ![]() |
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Full document | ![]() | 986.2 KB | Display | |
Data in XML | ![]() | 221.1 KB | Display | |
Data in CIF | ![]() | 337.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0545MC ![]() 0542C ![]() 0543C ![]() 0544C ![]() 0546C ![]() 0547C ![]() 0548C ![]() 0549C ![]() 0550C ![]() 0551C ![]() 6nyfC ![]() 6nygC ![]() 6nyjC ![]() 6nymC ![]() 6nynC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 3.9 TB Data #1: Helicobacter pylori vacuolating cytotoxin A [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 88463.211 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2c (OA-2c) Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.088 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: VacA OA-2c |
Specimen support | Details: unspecified |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 6 sec. / Electron dose: 7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 13708 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 30 / Used frames/image: 1-30 |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 540214 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D6 (2x6 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31700 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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