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- EMDB-22701: Structure of the EPEC type III secretion injectisome EspA filament -

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Basic information

Entry
Database: EMDB / ID: EMD-22701
TitleStructure of the EPEC type III secretion injectisome EspA filament
Map dataEPEC type III secretion injectisome EspA filament
Sample
  • Organelle or cellular component: EspA filament
    • Protein or peptide: Translocon EspA
KeywordsTransport / filament / secretion system / PROTEIN TRANSPORT
Function / homologyEspA-like secreted protein / EspA-like secreted protein / EspA/CesA-like / Translocon EspA
Function and homology information
Biological speciesEscherichia coli O127:H6 str. E2348/69 (bacteria) / Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsLyons BJE / Atkinson CE
Funding support Canada, 2 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Structure / Year: 2021
Title: Cryo-EM structure of the EspA filament from enteropathogenic Escherichia coli: Revealing the mechanism of effector translocation in the T3SS.
Authors: Bronwyn J E Lyons / Claire E Atkinson / Wanyin Deng / Antonio Serapio-Palacios / B Brett Finlay / Natalie C J Strynadka /
Abstract: The type III secretion system (T3SS) is a virulence mechanism employed by Gram-negative pathogens. The T3SS forms a proteinaceous channel that projects a needle into the extracellular medium where it ...The type III secretion system (T3SS) is a virulence mechanism employed by Gram-negative pathogens. The T3SS forms a proteinaceous channel that projects a needle into the extracellular medium where it interacts with the host cell to deliver virulence factors. Enteropathogenic Escherichia coli (EPEC) is unique in adopting a needle extension to the T3SS-a filament formed by EspA-which is absolutely required for efficient colonization of the gut. Here, we describe the cryoelectron microscopy structure of native EspA filaments from EPEC at 3.6-Å resolution. Within the filament, positively charged residues adjacent to a hydrophobic groove line the lumen of the filament in a spiral manner, suggesting a mechanism of substrate translocation mediated via electrostatics. Using structure-guided mutagenesis, in vivo studies corroborate the role of these residues in secretion and translocation function. The high-resolution structure of the EspA filament could aid in structure-guided drug design of antivirulence therapeutics.
History
DepositionSep 23, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k7k
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7k7k
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22701.png

Downloads & links

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Map

FileDownload / File: emd_22701.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEPEC type III secretion injectisome EspA filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.75 Å/pix.
x 250 pix.
= 437.5 Å		1.75 Å/pix.
x 250 pix.
= 437.5 Å		1.75 Å/pix.
x 250 pix.
= 437.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.05
Minimum - Maximum-0.18659714 - 0.31323308
Average (Standard dev.)0.00006124191 (±0.00854415)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 437.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.751.751.75
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z437.500437.500437.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.1870.3130.000

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Supplemental data

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Sample components

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Entire : EspA filament

EntireName: EspA filament
Components
  • Organelle or cellular component: EspA filament
    • Protein or peptide: Translocon EspA

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Supramolecule #1: EspA filament

SupramoleculeName: EspA filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria)

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Macromolecule #1: Translocon EspA

MacromoleculeName: Translocon EspA / type: protein_or_peptide / ID: 1 / Number of copies: 28 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC
Molecular weightTheoretical: 20.482811 KDa
SequenceString: MDTSTTASVA SANASTSTSM AYDLGSMSKD DVIDLFNKLG VFQAAILMFA YMYQAQSDLS IAKFADMNEA SKESTTAQKM ANLVDAKIA DVQSSSDKNA KAQLPDEVIS YINDPRNDIT ISGIDNINAQ LGAGDLQTVK AAISAKANNL TTTVNNSQLE I QQMSNTLN ...String:
MDTSTTASVA SANASTSTSM AYDLGSMSKD DVIDLFNKLG VFQAAILMFA YMYQAQSDLS IAKFADMNEA SKESTTAQKM ANLVDAKIA DVQSSSDKNA KAQLPDEVIS YINDPRNDIT ISGIDNINAQ LGAGDLQTVK AAISAKANNL TTTVNNSQLE I QQMSNTLN LLTSARSDMQ SLQYRTISGI SLGK

UniProtKB: Translocon EspA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 0.475 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 64.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 15523
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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