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

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Basic information

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


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / 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 / negative regulation of G protein-coupled receptor signaling pathway ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / 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 / negative regulation of G protein-coupled receptor signaling pathway / protein phosphatase inhibitor activity / negative regulation of protein import into nucleus / Frs2-mediated activation / glycosyltransferase activity / protein kinase inhibitor activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / transcription repressor complex / nucleotidyltransferase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / GTPase activator activity / protein sequestering activity / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / histone deacetylase binding / Negative regulation of MAPK pathway / 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 / Signaling by BRAF and RAF1 fusions / intracellular protein localization / melanosome / toxin activity / cadherin binding / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / cytoplasm / cytosol
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 ...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
CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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: 2.55 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)83,1535
Polymers82,3723
Non-polymers7812
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-37 kcal/mol
Surface area31030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.920, 56.770, 120.350
Angle α, β, γ (deg.)90.00, 126.45, 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-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N7O13P2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 50% MPD, 8% PEG 8000, 0.1M Sodium Cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.5→48.4 Å / Num. obs: 30578 / % possible obs: 99.2 % / Redundancy: 6 % / Biso Wilson estimate: 90.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4821 / CC1/2: 0.71 / % possible all: 97.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GN0

3gn0


Resolution: 2.55→48.4 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.455 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.425 / SU Rfree Blow DPI: 0.253 / SU Rfree Cruickshank DPI: 0.261
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1439 5 %RANDOM
Rwork0.215 ---
obs0.216 28770 99.7 %-
Displacement parametersBiso mean: 114.41 Å2
Baniso -1Baniso -2Baniso -3
1-19.5568 Å20 Å213.4289 Å2
2---12.5067 Å20 Å2
3----7.0502 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: 1 / Resolution: 2.55→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5205 0 52 26 5283
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015331HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.17180HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2567SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes7HARMONIC2
X-RAY DIFFRACTIONt_gen_planes928HARMONIC5
X-RAY DIFFRACTIONt_it5331HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion3.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion687SEMIHARMONIC5
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_contact6100SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.65 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2953 148 4.98 %
Rwork0.2798 2822 -
all0.2806 2970 -
obs--99.3 %

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