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- EMDB-22881: Cryo-EM structure of enteropathogenic Escherichia colitype III se... -

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Basic information

Entry
Database: EMDB / ID: EMD-22881
TitleCryo-EM structure of enteropathogenic Escherichia colitype III secretion system EspA filament
Map dataCryo-EM structure of enteropathogenic Escherichia coli type III secretion system EspA filament
Sample
  • Complex: EspA filament
    • Protein or peptide: Translocon EspA
Keywordstype III secretion system (T3SS) / EspA filament / Helical reconstruction / PROTEIN FIBRIL
Function / homologyEspA-like secreted protein / EspA-like secreted protein / EspA/CesA-like / Translocon EspA
Function and homology information
Biological speciesEscherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZheng W / Ilangovan A / Costa TRD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Cryoelectron-microscopy structure of the enteropathogenic type III secretion system EspA filament.
Authors: Weili Zheng / Alejandro Peña / Aravindan Ilangovan / Yasaman Naemi Baghshomali / Gad Frankel / Edward H Egelman / Tiago R D Costa /
Abstract: Enteropathogenic (EPEC) and enterohemorrhagic (EHEC) utilize a macromolecular type III secretion system (T3SS) to inject effector proteins into eukaryotic cells. This apparatus spans the inner and ...Enteropathogenic (EPEC) and enterohemorrhagic (EHEC) utilize a macromolecular type III secretion system (T3SS) to inject effector proteins into eukaryotic cells. This apparatus spans the inner and outer bacterial membranes and includes a helical needle protruding into the extracellular space. Thus far observed only in EPEC and EHEC and not found in other pathogenic Gram-negative bacteria that have a T3SS is an additional helical filament made by the EspA protein that forms a long extension to the needle, mediating both attachment to eukaryotic cells and transport of effector proteins through the intestinal mucus layer. Here, we present the structure of the EspA filament from EPEC at 3.4 Å resolution. The structure reveals that the EspA filament is a right-handed 1-start helical assembly with a conserved lumen architecture with respect to the needle to ensure the seamless transport of unfolded cargos en route to the target cell. This functional conservation is despite the fact that there is little apparent overall conservation at the level of sequence or structure with the needle. We also unveil the molecular details of the immunodominant EspA epitope that can now be exploited for the rational design of epitope display systems.
History
DepositionOct 22, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 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: 0.0225
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0225
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7khw
  • Surface level: 0.0225
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7khw
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22881.png

Downloads & links

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Map

FileDownload / File: emd_22881.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of enteropathogenic Escherichia coli type III secretion system EspA filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0225 / Movie #1: 0.0225
Minimum - Maximum-0.11183347 - 0.1699275
Average (Standard dev.)0.000070727314 (±0.008422199)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z276.480276.480276.480
α/β/γ90.00090.00090.000
start NX/NY/NZ937643
NX/NY/NZ114126230
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1120.1700.000

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Supplemental data

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Sample components

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Entire : EspA filament

EntireName: EspA filament
Components
  • Complex: EspA filament
    • Protein or peptide: Translocon EspA

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Supramolecule #1: EspA filament

SupramoleculeName: EspA filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC

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Macromolecule #1: Translocon EspA

MacromoleculeName: Translocon EspA / type: protein_or_peptide / ID: 1 / Number of copies: 50 / 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: 7.5
GridPretreatment - Type: PLASMA CLEANING / Details: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 159460
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION

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