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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8778 | |||||||||
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Title | Type II secretin from Enteropathogenic Escherichia coli - GspD | |||||||||
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![]() | Type 2 secretin / outer membrane complex / homo oligomer / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Hay ID / Belousoff MJ | |||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 85.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.9 KB 12.9 KB | Display Display | ![]() |
Images | ![]() | 54.9 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w68MC ![]() 8779C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Type II sectretin outer membrane complex
Entire | Name: Type II sectretin outer membrane complex |
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Components |
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-Supramolecule #1: Type II sectretin outer membrane complex
Supramolecule | Name: Type II sectretin outer membrane complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Putative type II secretion protein
Macromolecule | Name: Putative type II secretion protein / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: E2348/69 / EPEC |
Molecular weight | Theoretical: 41.192559 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GNSQVFYLKY SKAEDLVDVL KQVSGTLTAA KEEAEGTVGS GREVVSIAAS KHSNALIVTA PQDIMQSLQS VIEQLDIRRA QVHVEALIV EVAEGSNINF GVQWGSKDAG LMQFANGTQI PIGTLGAAIS AAKPQKGSTV ISENGATTIN PDTNGDLSTL A QLLSGFSG ...String: GNSQVFYLKY SKAEDLVDVL KQVSGTLTAA KEEAEGTVGS GREVVSIAAS KHSNALIVTA PQDIMQSLQS VIEQLDIRRA QVHVEALIV EVAEGSNINF GVQWGSKDAG LMQFANGTQI PIGTLGAAIS AAKPQKGSTV ISENGATTIN PDTNGDLSTL A QLLSGFSG TAVGVVKGDW MALVQAVKND SSSNVLSTPS ITTLDNQEAF FMVGQDVPVL TGSTVGSNNS NPFNTVERKK VG IMLKVTP QINEGNAVQM VIEQEVSKVE GQTSLDVVFG ERKLKTTVLA NDGELIVLGG LMDDQAGESV AKVPLLGDIP LIG NLFKST ADKKEKRNLM VFIRPTILRD GMAADGVSQR KYNYMRAEQI YRDEQGLSLM PHTAQPILPA Q UniProtKB: Putative type II secretion protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-18 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-5w68: |