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- PDB-9qhh: Lymphostatin - pH 8 - phosphate buffer -

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Basic information

Entry
Database: PDB / ID: 9qhh
TitleLymphostatin - pH 8 - phosphate buffer
ComponentsLymphostatin
KeywordsTOXIN / Lymphostatin virulence factor A/E bacteria Toxin-like
Function / homology
Function and homology information


glycosyltransferase activity / cysteine-type endopeptidase activity
Similarity search - Function
Protein of unknown function DUF3491 / Protein of unknown function (DUF3491) / Peptidase C58, YopT-type domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesEscherichia coli O127:H6 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGriessmann, M. / Schneider, R. / Rasmussen, T. / Bottcher, B.
Funding support Germany, United Kingdom, 6items
OrganizationGrant numberCountry
German Research Foundation (DFG)359471283 Germany
German Research Foundation (DFG)456578072 Germany
German Research Foundation (DFG)525040890 Germany
German Research Foundation (DFG)428774170 Germany
German Research Foundation (DFG)411346541 Germany
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/RL/230002C United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Structure of lymphostatin, a large multi-functional virulence factor of pathogenic Escherichia coli.
Authors: Matthias Griessmann / Tim Rasmussen / Vanessa J Flegler / Christian Kraft / Ronja Schneider / Max Hateley / Lukas Spantzel / Mark P Stevens / Michael Börsch / Bettina Böttcher /
Abstract: Lymphostatin is a key virulence factor of enteropathogenic and enterohaemorrhagic Escherichia coli, playing roles in bacterial colonisation of the gut and in the inhibition of lymphocyte ...Lymphostatin is a key virulence factor of enteropathogenic and enterohaemorrhagic Escherichia coli, playing roles in bacterial colonisation of the gut and in the inhibition of lymphocyte proliferation and proinflammatory responses. The protein's glycosyltransferase and cysteine protease motifs are required for activity against lymphocytes, but high-resolution structural information has proven elusive. Here, we describe the structure of lymphostatin from enteropathogenic E. coli O127:H6, determined by electron cryo-microscopy at different pH values. We observe three conformations of a highly complex molecule with two glycosyltransferase domains, one PaToxP-like protease domain, an ADP-ribosyltransferase domain, a vertex domain and a delivery domain. Long linkers hold these domains together and occlude the catalytic sites of the N-terminal glycosyltransferase and protease domains. Lymphostatin binds to bovine T-lymphocytes and HEK-293T cells, forming clusters at the plasma membrane that are internalized. With six distinct domains, lymphostatin can be regarded as a multitool of pathogenic Escherichia coli, enabling complex interactions with host cells.
History
DepositionMar 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lymphostatin


Theoretical massNumber of molelcules
Total (without water)366,4211
Polymers366,4211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Lymphostatin


Mass: 366421.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (bacteria) / Gene: lifA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RM48
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Lymphostatin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.366 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli O127:H6 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Details: 25 mM sodium phosphate pH 8, 100 mM NaCl, 0.075 mM MnCl2, 1.5 mM TCEP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
9cryoSPARC4.6initial Euler assignment
12RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1294835 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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