+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8779 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Type II secretin from Enteropathogenic Escherichia coli - GspD | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
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 (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Hay ID / Belousoff MJ | |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8779.map.gz | 16.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8779-v30.xml emd-8779.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8779_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_8779.png | 85.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8779 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8779 | HTTPS FTP |
-Validation report
Summary document | emd_8779_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_8779_full_validation.pdf.gz | 77.9 KB | Display | |
Data in XML | emd_8779_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8779 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8779 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_8779.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Type II secretin complex from E. coli O127:H6 strain E2348/69 - GspD
Entire | Name: Type II secretin complex from E. coli O127:H6 strain E2348/69 - GspD |
---|---|
Components |
|
-Supramolecule #1: Type II secretin complex from E. coli O127:H6 strain E2348/69 - GspD
Supramolecule | Name: Type II secretin complex from E. coli O127:H6 strain E2348/69 - GspD type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: O127:H6 strain E2348/69 |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: C43 |
-Macromolecule #1: GspD
Macromolecule | Name: GspD / type: protein_or_peptide / ID: 1 / Details: Homo pentadecamer of GspD bacterial secretin / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: O127:H6 strain E2348/69 |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MFWRDMTLSI WRKKTTGLKT KKRLLPLMLA AALCSSPVWA EEATFTANFK DTDLKSFIET VGANLNKTI IMGPGVQGKV SIRTMTPLNE RQYYQLFLNL LEAQGYAVVP MENDVLKVVK S SAAKVEPL PLVGEGSDNY AGDEMVTKVV PVRNVSVREL APILRQMIDS ...String: MFWRDMTLSI WRKKTTGLKT KKRLLPLMLA AALCSSPVWA EEATFTANFK DTDLKSFIET VGANLNKTI IMGPGVQGKV SIRTMTPLNE RQYYQLFLNL LEAQGYAVVP MENDVLKVVK S SAAKVEPL PLVGEGSDNY AGDEMVTKVV PVRNVSVREL APILRQMIDS AGSGNVVNYD PS NVIMLTG RASVVERLTE VIQRVDHAGN RTEEVIPLDN ASASEIARVL ESLTKNSGEN QPA TLKSQI VADERTNSVI VSGDPATRDK MRRLIRRLDS EMERSGNSQV FYLKYSKAED LVDV LKQVS GTLTAAKEEA EGTVGSGREV VSIAASKHSN ALIVTAPQDI MQSLQSVIEQ LDIRR AQVH VEALIVEVAE GSNINFGVQW GSKDAGLMQF ANGTQIPIGT LGAAISAAKP QKGSTV ISE NGATTINPDT NGDLSTLAQL LSGFSGTAVG VVKGDWMALV QAVKNDSSSN VLSTPSI TT LDNQEAFFMV GQDVPVLTGS TVGSNNSNPF NTVERKKVGI MLKVTPQINE GNAVQMVI E QEVSKVEGQT SLDVVFGERK LKTTVLANDG ELIVLGGLMD DQAGESVAKV PLLGDIPLI GNLFKSTADK KEKRNLMVFI RPTILRDGMA ADGVSQRKYN YMRAEQIYRD EQGLSLMPHT AQPILPAQ |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
---|---|
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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-7 / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 127000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 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 |