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- PDB-7k7k: Structure of the EPEC type III secretion injectisome EspA filament -

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Basic information

Entry
Database: PDB / ID: 7k7k
TitleStructure of the EPEC type III secretion injectisome EspA filament
ComponentsTranslocon EspA
KeywordsPROTEIN TRANSPORT / Transport / filament / secretion system
Function / homologyEspA-like secreted protein / EspA-like secreted protein / EspA/CesA-like / Translocon EspA
Function and homology information
Biological speciesEscherichia coli O127:H6 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsLyons, B.J.E. / Atkinson, C.E. / Strynadka, N.C.J.
Funding support Canada, 2items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.title
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Translocon EspA
B: Translocon EspA
C: Translocon EspA
D: Translocon EspA
E: Translocon EspA
F: Translocon EspA
G: Translocon EspA
H: Translocon EspA
I: Translocon EspA
J: Translocon EspA
K: Translocon EspA
L: Translocon EspA
M: Translocon EspA
N: Translocon EspA
O: Translocon EspA
P: Translocon EspA
Q: Translocon EspA
R: Translocon EspA
S: Translocon EspA
T: Translocon EspA
U: Translocon EspA
V: Translocon EspA
W: Translocon EspA
X: Translocon EspA
Y: Translocon EspA
Z: Translocon EspA
a: Translocon EspA
b: Translocon EspA


Theoretical massNumber of molelcules
Total (without water)573,51928
Polymers573,51928
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area114040 Å2
ΔGint-668 kcal/mol
Surface area216020 Å2

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Components

#1: Protein ...
Translocon EspA


Mass: 20482.811 Da / Num. of mol.: 28 / Source method: isolated from a natural source
Source: (natural) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC / References: UniProt: B7UM94

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: EspA filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 0.475 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 64.3 ° / Axial rise/subunit: 4.4 Å / Axial symmetry: C1
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15523 / Symmetry type: HELICAL

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