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- PDB-6gn0: Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-... -

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Basic information

Entry
Database: PDB / ID: 6gn0
TitleExoenzyme S from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta, tetrameric crystal form
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
14-3-3 protein beta/alpha / Exoenzyme S / 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. / 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 29, 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: 14-3-3 protein beta/alpha
D: 14-3-3 protein beta/alpha
E: Exoenzyme S
F: Exoenzyme S
G: Exoenzyme S
H: Exoenzyme S


Theoretical massNumber of molelcules
Total (without water)219,1168
Polymers219,1168
Non-polymers00
Water0
1
A: 14-3-3 protein beta/alpha
B: 14-3-3 protein beta/alpha
E: Exoenzyme S
G: Exoenzyme S


Theoretical massNumber of molelcules
Total (without water)109,5584
Polymers109,5584
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-37 kcal/mol
Surface area40010 Å2
MethodPISA
2
C: 14-3-3 protein beta/alpha
D: 14-3-3 protein beta/alpha
F: Exoenzyme S
H: Exoenzyme S


Theoretical massNumber of molelcules
Total (without water)109,5584
Polymers109,5584
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-33 kcal/mol
Surface area40100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.200, 168.760, 82.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 28565.977 Da / Num. of mol.: 4
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.: 4 / 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: Q51451, UniProt: Q93SQ1*PLUS

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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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 12% PEG 3350, 4% Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.24→118.1 Å / Num. all: 254184 / Num. obs: 37506 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 52.97 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.505 / Net I/σ(I): 5
Reflection shellResolution: 3.24→3.29 Å / Redundancy: 14 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1875 / CC1/2: 0.53 / Rrim(I) all: 2.396 / % possible all: 96.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C23

2c23


Resolution: 3.24→118.05 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.813 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.557
RfactorNum. reflection% reflectionSelection details
Rfree0.2944 1830 4.93 %RANDOM
Rwork0.2435 ---
obs0.246 37156 99 %-
Displacement parametersBiso mean: 54.42 Å2
Baniso -1Baniso -2Baniso -3
1-3.9417 Å20 Å20 Å2
2---8.4334 Å20 Å2
3---4.4917 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: 1 / Resolution: 3.24→118.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13303 0 0 0 13303
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113471HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1918112HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6488SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2367HARMONIC5
X-RAY DIFFRACTIONt_it13471HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion3.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1716SEMIHARMONIC5
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_contact15944SEMIHARMONIC4
LS refinement shellResolution: 3.24→3.33 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.3577 142 5.12 %
Rwork0.2955 2632 -
all0.2987 2774 -
obs--97.22 %

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