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- PDB-29jd: NMR Structure of the Calcium bound form of OutG, major pilin from... -

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Basic information

Entry
Database: PDB / ID: 29jd
TitleNMR Structure of the Calcium bound form of OutG, major pilin from Dickeya dadantii T2SS
ComponentsType II secretion system core protein G
KeywordsPROTEIN TRANSPORT / Dickeya dadantii T2SS / major pilin / pilus / secretion
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / protein processing / plasma membrane
Similarity search - Function
Type II secretion system protein GspG / Type II secretion system protein GspG, C-terminal / Type II secretion system (T2SS), protein G / Bacterial general secretion pathway protein G-type pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Type II secretion system core protein G
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBardiaux, B. / Jacobsen, T. / Dazzoni, R. / Nilges, M. / Francetic, O. / Shevchik, V. / Izadi-Pruneyre, N.
Funding supportEuropean Union, France, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765042European Union
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0020-01 France
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 16, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2026Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5912
Polymers13,5511
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Type II secretion system core protein G


Mass: 13550.833 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (bacteria) / Gene: outG, Dda3937_02418 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E0SM38
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / 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: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HN(CA)CO
141isotropic13D HNCA
151isotropic13D HN(CO)CA
161isotropic13D HN(CA)CB
171isotropic13D HN(COCA)CB
181isotropic13D C(CO)NH
191isotropic13D H(CCO)NH
1101isotropic12D 1H-13C HSQC
1111isotropic13D (H)CCH-TOCSY
1121isotropic13D 1H-15N NOESY
1131isotropic23D 1H-13C NOESY
1141isotropic22D (HB)CB(CGCD)HD
1151isotropic22D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsType: solution
Contents: 0.43 mM [U-13C; U-15N] OutG, 100 mM NaCl, 5 mM CaCl2, 50 mM HEPES, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O
Label: sample_1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.43 mMOutG[U-13C; U-15N]1
100 mMNaClnatural abundance1
5 mMCaCl2natural abundance1
50 mMHEPESnatural abundance1
95 %H2Onatural abundance1
5 %D2O[U-2H]1
Sample conditionsIonic strength: 0.05 M / Label: sample_conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD6001
Bruker AVANCE NEOBrukerAVANCE NEO8002

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.5.1CCPNchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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