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- PDB-2mky: Structure of the PrgK first periplasmic domain -

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Database: PDB / ID: 2mky
TitleStructure of the PrgK first periplasmic domain
ComponentsPathogenicity 1 island effector protein
KeywordsCELL INVASION / Secretion systems / macromolecular assemblies
Function / homologyHypothetical protein rpa1041 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesSalmonella enterica (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBergeron, J. / Mcintosh, L. / Strynadka, N.
CitationJournal: Structure / Year: 2015
Title: The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body.
Authors: Julien R C Bergeron / Liam J Worrall / Soumya De / Nikolaos G Sgourakis / Adrienne H Cheung / Emilie Lameignere / Mark Okon / Gregory A Wasney / David Baker / Lawrence P McIntosh / Natalie C J Strynadka /
Abstract: The type III secretion system (T3SS) is a large macromolecular assembly found at the surface of many pathogenic Gram-negative bacteria. Its role is to inject toxic "effector" proteins into the cells ...The type III secretion system (T3SS) is a large macromolecular assembly found at the surface of many pathogenic Gram-negative bacteria. Its role is to inject toxic "effector" proteins into the cells of infected organisms. The molecular details of the assembly of this large, multimembrane-spanning complex remain poorly understood. Here, we report structural, biochemical, and functional analyses of PrgK, an inner-membrane component of the prototypical Salmonella typhimurium T3SS. We have obtained the atomic structures of the two ring building globular domains and show that the C-terminal transmembrane helix is not essential for assembly and secretion. We also demonstrate that structural rearrangement of the two PrgK globular domains, driven by an interconnecting linker region, may promote oligomerization into ring structures. Finally, we used electron microscopy-guided symmetry modeling to propose a structural model for the intimately associated PrgH-PrgK ring interaction within the assembled basal body.
DepositionFeb 14, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references

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Deposited unit
A: Pathogenicity 1 island effector protein

Theoretical massNumber of molelcules
Total (without water)6,5321

  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy


#1: Protein Pathogenicity 1 island effector protein

Mass: 6532.363 Da / Num. of mol.: 1 / Fragment: UNP residues 19-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: subsp. enterica serovar Typhimurium str. DT2 / Gene: prgK, STMDT2_27711 / Production host: Escherichia coli (E. coli) / References: UniProt: U4MER0

Experimental details


ExperimentMethod: SOLUTION NMR
NMR experiment
1112D 1H-15N HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1813D H(CCO)NH
1912D 1H-13C HSQC aromatic
11013D 1H-13C NOESY aliphatic
11113D 1H-15N NOESY
11213D 1H-13C NOESY

Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] PrgK, 10 % D2O, 25 mM HEPES, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPrgK-1[U-100% 13C; U-100% 15N]1
10 %D2O-21
25 mMHEPES-31
Sample conditionsIonic strength: 0 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8501
Bruker AvanceBrukerAvance6002


NMR software
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1912 / NOE intraresidue total count: 147 / NOE long range total count: 272 / NOE medium range total count: 296 / NOE sequential total count: 1197 / Protein phi angle constraints total count: 50 / Protein psi angle constraints total count: 51
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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