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- EMDB-8779: Type II secretin from Enteropathogenic Escherichia coli - GspD -

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Basic information

Entry
Database: EMDB / ID: EMD-8779
TitleType II secretin from Enteropathogenic Escherichia coli - GspD
Map data
Sample
  • Complex: Type II secretin complex from E. coli O127:H6 strain E2348/69 - GspD
    • Protein or peptide: GspD
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
Type II secretion system protein GspD / GspD/PilQ family / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein
Similarity search - Domain/homology
Putative type II secretion protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsHay ID / Belousoff MJ
CitationJournal: 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
DepositionJun 16, 2017-
Header (metadata) releaseJul 5, 2017-
Map releaseNov 15, 2017-
UpdateFeb 21, 2018-
Current statusFeb 21, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8779.png

Downloads & links

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Map

FileDownload / File: emd_8779.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 1.1 / Movie #1: 1.1
Minimum - Maximum-4.874773 - 9.209163999999999
Average (Standard dev.)0.046800718 (±0.29851186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z330.000330.000330.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-59-19-84
NX/NY/NZ8052101
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-4.8759.2090.047

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Supplemental data

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Sample components

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Entire : Type II secretin complex from E. coli O127:H6 strain E2348/69 - GspD

EntireName: Type II secretin complex from E. coli O127:H6 strain E2348/69 - GspD
Components
  • Complex: Type II secretin complex from E. coli O127:H6 strain E2348/69 - GspD
    • Protein or peptide: GspD

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Supramolecule #1: Type II secretin complex from E. coli O127:H6 strain E2348/69 - GspD

SupramoleculeName: 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 expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: C43

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Macromolecule #1: GspD

MacromoleculeName: 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 expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 127000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-7 / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 100000
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 0.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 0.4)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C15 (15 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.40) / Number images used: 43500
FSC plot (resolution estimation)

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