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- EMDB-8778: Type II secretin from Enteropathogenic Escherichia coli - GspD -

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Basic information

Entry
Database: EMDB / ID: EMD-8778
TitleType II secretin from Enteropathogenic Escherichia coli - GspD
Map data
Sample
  • Complex: Type II sectretin outer membrane complex
    • Protein or peptide: Putative type II secretion protein
KeywordsType 2 secretin / outer membrane complex / homo oligomer / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane
Similarity search - Function
Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / 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) / Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHay ID / Belousoff MJ
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1092262 Australia
Australian Research Council (ARC)FL130100038 Australia
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-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5w68
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8778.png

Downloads & links

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Map

FileDownload / File: emd_8778.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 288 pix.
= 305.28 Å		1.06 Å/pix.
x 288 pix.
= 305.28 Å		1.06 Å/pix.
x 288 pix.
= 305.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.71180654 - 1.3726916
Average (Standard dev.)0.0031074425 (±0.049994852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 305.27997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z305.280305.280305.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-179-179-179
NX/NY/NZ359359359
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.7121.3730.003

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Supplemental data

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Sample components

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Entire : Type II sectretin outer membrane complex

EntireName: Type II sectretin outer membrane complex
Components
  • Complex: Type II sectretin outer membrane complex
    • Protein or peptide: Putative type II secretion protein

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Supramolecule #1: Type II sectretin outer membrane complex

SupramoleculeName: Type II sectretin outer membrane complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: O127:H6 strain E2348/69

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Macromolecule #1: Putative type II secretion protein

MacromoleculeName: Putative type II secretion protein / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC
Molecular weightTheoretical: 41.192559 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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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 / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen 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

Particle selectionNumber selected: 20000
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.4) / Number images used: 8896
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 0.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 0.4)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5w68:
Type II secretin from Enteropathogenic Escherichia coli - GspD

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