[English] 日本語
Yorodumi- PDB-6gnk: Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gnk | ||||||
---|---|---|---|---|---|---|---|
Title | Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta, trimeric crystal form bound to Carba-NAD | ||||||
Components |
| ||||||
Keywords | TOXIN / 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 | ||||||
Biological species | Homo sapiens (human) Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Karlberg, T. / Pinto, A.F. / Hornyak, P. / Thorsell, A.G. / Nareoja, K. / Schuler, H. | ||||||
Funding support | Sweden, 1items
| ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6gnk.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6gnk.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 6gnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/6gnk ftp://data.pdbj.org/pub/pdb/validation_reports/gn/6gnk | HTTPS FTP |
---|
-Related structure data
Related structure data | 6gn0C 6gn8C 6gnjC 6gnnC 3gn0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | 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 | | 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 / | #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.17 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 50% MPD, 8% PEG 8000, 0.1M Sodium Cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 114.41 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.55→48.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.55→2.65 Å / Total num. of bins used: 14
|