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- PDB-6gnn: Exoenzyme T from Pseudomonas aeruginosa in complex with human 14-... -

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Basic information

Entry
Database: PDB / ID: 6gnn
TitleExoenzyme T from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta, tetrameric crystal form bound to STO1101
Components
  • 14-3-3 protein beta/alpha
  • Exoenzyme T
KeywordsTOXIN / EXOT / PSEUDOMONAS AERUGINOSA / ADP-RIBOSYLATION / NAD
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase / negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / NAD+-protein-arginine ADP-ribosyltransferase activity / 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 ...NAD+-protein-arginine ADP-ribosyltransferase / negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / NAD+-protein-arginine ADP-ribosyltransferase activity / 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 / positive regulation of catalytic activity / protein kinase inhibitor activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / NAD+-protein poly-ADP-ribosyltransferase activity / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / 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 / 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 / melanosome / toxin activity / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / extracellular exosome / extracellular region / identical protein binding / 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 / 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 T
Similarity search - Component
Biological speciesHomo sapiens (human)
Pseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 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
C: Exoenzyme T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5553
Polymers55,2902
Non-polymers2641
Water00
1
A: 14-3-3 protein beta/alpha
C: Exoenzyme T
hetero molecules

A: 14-3-3 protein beta/alpha
C: Exoenzyme T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1096
Polymers110,5804
Non-polymers5292
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-x+2,-y+3,z1
Buried area8130 Å2
ΔGint-43 kcal/mol
Surface area39650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.378, 60.301, 81.190
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.: 1
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 T


Mass: 26724.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 / Gene: exoT, PA0044 / Plasmid: pET Duet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I788
#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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 12% PEG 6000, 0.1M Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.79→57.7 Å / Num. obs: 6026 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.062 / Rrim(I) all: 0.215 / Net I/σ(I): 7.3
Reflection shellResolution: 3.79→3.85 Å / Redundancy: 12.2 % / Rmerge(I) obs: 2.298 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 351 / CC1/2: 0.515 / Rpim(I) all: 0.681 / Rrim(I) all: 2.399 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GN0

6gn0


Resolution: 3.79→53.442 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.79
RfactorNum. reflection% reflectionSelection details
Rfree0.3849 313 5.29 %Random selection
Rwork0.2852 ---
obs0.2903 5915 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.79→53.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 18 0 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033370
X-RAY DIFFRACTIONf_angle_d0.5894537
X-RAY DIFFRACTIONf_dihedral_angle_d4.782051
X-RAY DIFFRACTIONf_chiral_restr0.036494
X-RAY DIFFRACTIONf_plane_restr0.003599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7895-4.7740.46971520.35732710X-RAY DIFFRACTION98
4.774-53.44720.33861610.25282892X-RAY DIFFRACTION99

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