+Open data
-Basic information
Entry | Database: PDB / ID: 5w68 | |||||||||
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Title | Type II secretin from Enteropathogenic Escherichia coli - GspD | |||||||||
Components | Putative type II secretion protein | |||||||||
Keywords | MEMBRANE PROTEIN / Type 2 secretin / outer membrane complex / homo oligomer | |||||||||
Function / homology | Function and homology information protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane / membrane => GO:0016020 Similarity search - Function | |||||||||
Biological species | Escherichia coli O127:H6 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Hay, I.D. / Belousoff, M.J. / Dunstan, R. / Bamert, R. / Lithgow, T. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: J Bacteriol / Year: 2018 Title: Structure and Membrane Topography of the Vibrio-Type Secretin Complex from the Type 2 Secretion System of Enteropathogenic Escherichia coli. Authors: Iain D Hay / Matthew J Belousoff / Rhys A Dunstan / Rebecca S Bamert / Trevor Lithgow / Abstract: The β-barrel assembly machinery (BAM) complex is the core machinery for the assembly of β-barrel membrane proteins, and inhibition of BAM complex activity is lethal to bacteria. Discovery of ...The β-barrel assembly machinery (BAM) complex is the core machinery for the assembly of β-barrel membrane proteins, and inhibition of BAM complex activity is lethal to bacteria. Discovery of integral membrane proteins that are key to pathogenesis and yet do not require assistance from the BAM complex raises the question of how these proteins assemble into bacterial outer membranes. Here, we address this question through a structural analysis of the type 2 secretion system (T2SS) secretin from enteropathogenic O127:H6 strain E2348/69. Long β-strands assemble into a barrel extending 17 Å through and beyond the outer membrane, adding insight to how these extensive β-strands are assembled into the outer membrane. The substrate docking chamber of this secretin is shown to be sufficient to accommodate the substrate mucinase SteC. In order to cause disease, bacterial pathogens inhibit immune responses and induce pathology that will favor their replication and dissemination. In Gram-negative bacteria, these key attributes of pathogenesis depend on structures assembled into or onto the outer membrane. One of these is the T2SS. The -type T2SS mediates cholera toxin secretion in , and in O127:H6 strain E2348/69, the same machinery mediates secretion of the mucinases that enable the pathogen to penetrate intestinal mucus and thereby establish deadly infections. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5w68.cif.gz | 841.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w68.ent.gz | 711.9 KB | Display | PDB format |
PDBx/mmJSON format | 5w68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w68_validation.pdf.gz | 950.3 KB | Display | wwPDB validaton report |
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Full document | 5w68_full_validation.pdf.gz | 1000.9 KB | Display | |
Data in XML | 5w68_validation.xml.gz | 127.9 KB | Display | |
Data in CIF | 5w68_validation.cif.gz | 166 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/5w68 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/5w68 | HTTPS FTP |
-Related structure data
Related structure data | 8778MC 8779C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 41192.559 Da / Num. of mol.: 15 / Fragment: UNP residues 282-668 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) Strain: E2348/69 / EPEC / Gene: gspD, E2348C_3249 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: B7UI37 |
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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 |
-Sample preparation
Component | Name: Type II sectretin outer membrane complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: O127:H6 strain E2348/69 |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: C43 / Plasmid: pET20b |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 130000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF |
Image scans | Movie frames/image: 18 / Used frames/image: 1-18 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 20000 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C15 (15 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8896 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |