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- PDB-11mf: Cryo-EM of T2SS PulG pilus -

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Basic information

Entry
Database: PDB / ID: 11mf
TitleCryo-EM of T2SS PulG pilus
ComponentsType II secretion system core protein G
KeywordsPROTEIN FIBRIL / Endopilus / T2SS / PulG
Function / homology:
Function and homology information
Biological speciesKlebsiella oxytoca (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSonani, R.R. / Lejeune, M. / Ivashchenko, S. / Bardiaux, B. / Vos, M. / Francetic, O. / Shevchik, V.E. / Izadi-Pruneyre, N. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Structure / Year: 2026
Title: Structural determinants of endopilus assembly, stability, and functional specificity in bacterial type II secretion.
Authors: Maylis Lejeune / Stefaniia Ivashchenko / Régine Dazzoni / Benjamin Bardiaux / Ravi R Sonani / Matthijn Vos / Theis Jacobsen / Edward H Egelman / Michael Nilges / Olivera Francetic / ...Authors: Maylis Lejeune / Stefaniia Ivashchenko / Régine Dazzoni / Benjamin Bardiaux / Ravi R Sonani / Matthijn Vos / Theis Jacobsen / Edward H Egelman / Michael Nilges / Olivera Francetic / Vladimir E Shevchik / Nadia Izadi-Pruneyre /
Abstract: Gram-negative bacteria employ the type II secretion system (T2SS) to transport folded protein effectors via a periplasmic helical polymer called the endopilus, composed of one major and four minor ...Gram-negative bacteria employ the type II secretion system (T2SS) to transport folded protein effectors via a periplasmic helical polymer called the endopilus, composed of one major and four minor pilin subunits. Endopili resemble type IV pili but feature a conserved calcium-binding site stabilizing their major pilins. Endopilus polymerization is coupled to substrate translocation through a dedicated outer membrane channel. We compared T2SSs from plant and human pathogens, Dickeya dadantii and Klebsiella oxytoca, respectively. Despite different ecological niches and secreted effectors, their major pilins (OutG and PulG) share >77% sequence identity. Using NMR and cryo-EM, we solved structures of calcium-bound OutG monomer, as well as OutG and PulG endopili at 3.6 Å resolution. Combining structural, mutational, and biophysical analyses with in vivo assays, we identified key determinants of secretion specificity and endopilus stability. Our findings reveal how minor sequence variations in conserved nanomachines drive functional adaptation to diverse environments.
History
DepositionMar 4, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type II secretion system core protein G
B: Type II secretion system core protein G
C: Type II secretion system core protein G
D: Type II secretion system core protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9648
Polymers56,8044
Non-polymers1604
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
Type II secretion system core protein G


Mass: 14200.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: AB185_31145 / Production host: Escherichia coli (E. coli) / References: UniProt: A0ABF7PG33
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: PulG T2SS filament / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Klebsiella oxytoca (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.15.2_3472model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 83.46 ° / Axial rise/subunit: 10.46 Å / Axial symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 323409 / Symmetry type: HELICAL

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