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- PDB-6gnj: Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-... -

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Basic information

Entry
Database: PDB / ID: 6gnj
TitleExoenzyme S from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta, trimeric crystal form in complex with STO1101
Components
  • 14-3-3 protein beta/alpha
  • Exoenzyme S
KeywordsTOXIN / EXOS / PSEUDOMONAS AERUGINOSA / ADP-RIBOSYLATION / NAD
Function / homology
Function and homology information


negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling ...negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / Frs2-mediated activation / protein kinase inhibitor activity / positive regulation of catalytic activity / glycosyltransferase activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / protein targeting / Activation of BAD and translocation to mitochondria / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / nucleotidyltransferase activity / GTPase activator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Negative regulation of MAPK pathway / histone deacetylase binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / melanosome / Signaling by BRAF and RAF1 fusions / toxin activity / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / extracellular exosome / extracellular region / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. ...Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-F4W / 14-3-3 protein beta/alpha / Exoenzyme S
Similarity search - Component
Biological speciesHomo sapiens (human)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsKarlberg, T. / Pinto, A.F. / Hornyak, P. / Thorsell, A.G. / Nareoja, K. / Schuler, H.
Funding support Sweden, 1items
OrganizationGrant numberCountry
SB12-0022 Sweden
CitationJournal: Nat Commun / Year: 2018
Title: 14-3-3 proteins activate Pseudomonas exotoxins-S and -T by chaperoning a hydrophobic surface.
Authors: Karlberg, T. / Hornyak, P. / Pinto, A.F. / Milanova, S. / Ebrahimi, M. / Lindberg, M. / Pullen, N. / Nordstrom, A. / Loverli, E. / Caraballo, R. / Wong, E.V. / Nareoja, K. / Thorsell, A.G. / ...Authors: Karlberg, T. / Hornyak, P. / Pinto, A.F. / Milanova, S. / Ebrahimi, M. / Lindberg, M. / Pullen, N. / Nordstrom, A. / Loverli, E. / Caraballo, R. / Wong, E.V. / Nareoja, K. / Thorsell, A.G. / Elofsson, M. / De La Cruz, E.M. / Bjorkegren, C. / Schuler, H.
History
DepositionMay 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein beta/alpha
B: 14-3-3 protein beta/alpha
C: Exoenzyme S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6364
Polymers82,3723
Non-polymers2641
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-27 kcal/mol
Surface area31080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.398, 59.357, 120.641
Angle α, β, γ (deg.)90.00, 125.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 14-3-3 protein beta/alpha / Protein 1054 / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 28079.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAB / Plasmid: pET Duet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31946
#2: Protein Exoenzyme S


Mass: 26212.963 Da / Num. of mol.: 1 / Mutation: E379A, E381A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: exoS / Plasmid: pET Duet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93SQ1
#3: Chemical ChemComp-F4W / 3-(12-oxidanylidene-7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(8),2(6),9-trien-10-yl)propanoic acid


Mass: 264.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O3S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 40% MPD, 7% PEG 8000, 0.1M Sodium Cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 3.24→50 Å / Num. obs: 14937 / % possible obs: 98.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 128.4 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.351 / Net I/σ(I): 5.1
Reflection shellResolution: 3.24→3.43 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.73 / Mean I/σ(I) obs: 1 / Num. unique obs: 2326 / CC1/2: 0.468 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GN0

6gn0


Resolution: 3.24→48.9 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.416
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1037 7 %RANDOM
Rwork0.173 ---
obs0.177 14809 99.1 %-
Displacement parametersBiso mean: 102.55 Å2
Baniso -1Baniso -2Baniso -3
1--14.8364 Å20 Å221.2042 Å2
2---1.3912 Å20 Å2
3---16.2276 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 3.24→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5281 0 18 0 5299
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015372HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.167225HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2605SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes7HARMONIC2
X-RAY DIFFRACTIONt_gen_planes934HARMONIC5
X-RAY DIFFRACTIONt_it5372HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion3.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion686SEMIHARMONIC5
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_contact6134SEMIHARMONIC4
LS refinement shellResolution: 3.24→3.5 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2732 205 6.98 %
Rwork0.2534 2730 -
all0.2547 2935 -
obs--96.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.31520.73961.40751.96040.86053.64640.19260.1297-0.17730.15870.1463-0.2458-0.07240.3892-0.3389-0.15040.01730.0094-0.2725-0.0375-0.1236151.589323.582916.2766
21.77750.06711.31083.31562.67685.4904-0.247-0.30460.12220.2877-0.17340.1827-0.4905-0.66460.4204-0.18380.1090.0413-0.0899-0.0762-0.3296148.241341.428750.2138
32.09641.04560.4951.3158-0.1930.81710.1922-0.43210.0450.28540.03450.18920.141-0.268-0.2267-0.083-0.04330.0305-0.0828-0.0438-0.07116.00088.914315.4244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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