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- PDB-7khw: Cryo-EM structure of enteropathogenic Escherichia coli type III s... -

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Basic information

Entry
Database: PDB / ID: 7khw
TitleCryo-EM structure of enteropathogenic Escherichia coli type III secretion system EspA filament
ComponentsTranslocon EspA
KeywordsPROTEIN FIBRIL / type III secretion system (T3SS) / EspA filament / Helical reconstruction
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: 3.4 Å
AuthorsZheng, W. / Ilangovan, A. / Costa, T.R.D. / Egelman, E.H.
Funding support United States, 1items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Structure summary / Category: audit_author
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
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


Theoretical massNumber of molelcules
Total (without water)1,024,14150
Polymers1,024,14150
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area239830 Å2
ΔGint-1339 kcal/mol
Surface area364150 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 50 / Rise per n subunits: 4.4 Å / Rotation per n subunits: 64.3 °)

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Components

#1: Protein ...
Translocon EspA


Mass: 20482.811 Da / Num. of mol.: 50 / 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: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen 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 FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN2particle selection
4CTFFIND3CTF correction
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 64.3 ° / Axial rise/subunit: 4.4 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159460 / Symmetry type: HELICAL

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