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- PDB-4oyc: Crystal structure of the PrgK periplasmic domain 2 -

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Database: PDB / ID: 4oyc
TitleCrystal structure of the PrgK periplasmic domain 2
ComponentsLipoprotein PrgK
KeywordsPROTEIN TRANSPORT / T3SS / macromolecular assembly / inner-membrane
Function / homology
Function and homology information

protein secretion / cell outer membrane / integral component of membrane
Similarity search - Function
Type III secretion system lipoprotein HrcJ/YscJ / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / ANL, C-terminal domain / GMP Synthetase; Chain A, domain 3 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
AuthorsBergeron, J.R.C. / Strynadka, N.C.J.
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 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations

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Deposited unit
A: Lipoprotein PrgK
B: Lipoprotein PrgK

Theoretical massNumber of molelcules
Total (without water)24,0152
A: Lipoprotein PrgK

Theoretical massNumber of molelcules
Total (without water)12,0071
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
B: Lipoprotein PrgK

Theoretical massNumber of molelcules
Total (without water)12,0071
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.190, 34.740, 64.030
Angle α, β, γ (deg.)90.00, 110.77, 90.00
Int Tables number5
Space group name H-MC121
DetailsOligomeric state is 24-mer as determined by Electron Microscopy


#1: Protein Lipoprotein PrgK

Mass: 12007.386 Da / Num. of mol.: 2 / Fragment: 96-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: prgK, STM2871 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41786
#2: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION

Sample preparation

CrystalDensity Matthews: 1.67 Å3/Da / Density % sol: 26.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate pH 5.5, 20 % PEG 6000, 50 mM NaCl, 50 mM MgCl2

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→36.09 Å / Num. obs: 4992 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 54.04 Å2 / Net I/σ(I): 4.5


XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YJ7
Resolution: 2.6→36.09 Å / Cor.coef. Fo:Fc: 0.8703 / Cor.coef. Fo:Fc free: 0.8491 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.341
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 276 5.53 %RANDOM
Rwork0.2273 ---
obs0.229 4992 98.95 %-
Displacement parametersBiso mean: 48.68 Å2
Baniso -1Baniso -2Baniso -3
1-14.7306 Å20 Å2-0.3369 Å2
2---33.1022 Å20 Å2
3---18.3717 Å2
Refine analyzeLuzzati coordinate error obs: 0.381 Å
Refinement stepCycle: LAST / Resolution: 2.6→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 0 7 1344
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion20.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion181SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1455SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3191 72 5.26 %
Rwork0.2513 1296 -
all0.2551 1368 -
obs--98.95 %

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