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Yorodumi- PDB-6ggr: Crystal structure of Salmonella zinc metalloprotease effector Gtg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ggr | |||||||||||||||
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Title | Crystal structure of Salmonella zinc metalloprotease effector GtgA in complex with p65 | |||||||||||||||
Components |
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Keywords | METAL BINDING PROTEIN / Protease / Metalloprotease / zinc | |||||||||||||||
Function / homology | Function and homology information SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation ...SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / positive regulation of chondrocyte differentiation / Interleukin-1 signaling / acetaldehyde metabolic process / Downstream TCR signaling / prolactin signaling pathway / NF-kappaB p50/p65 complex / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / negative regulation of protein sumoylation / defense response to tumor cell / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / actinin binding / cellular response to angiotensin / response to UV-B / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / response to cobalamin / positive regulation of T cell receptor signaling pathway / non-canonical NF-kappaB signal transduction / phosphate ion binding / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / NF-kappaB binding / hair follicle development / positive regulation of vascular endothelial growth factor production / neuropeptide signaling pathway / canonical NF-kappaB signal transduction / RNA polymerase II core promoter sequence-specific DNA binding / response to amino acid / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of interleukin-12 production / negative regulation of insulin receptor signaling pathway / negative regulation of angiogenesis / negative regulation of miRNA transcription / liver development / positive regulation of interleukin-1 beta production / response to cytokine / positive regulation of interleukin-8 production / response to ischemia / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / response to bacterium / protein catabolic process / response to insulin / negative regulation of protein catabolic process / chromatin DNA binding / defense response / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / histone deacetylase binding / cellular response to hydrogen peroxide / cellular response to nicotine / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / chromatin organization / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / DNA-templated transcription Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å | |||||||||||||||
Authors | Jennings, E. / Esposito, D. / Rittinger, K. / Thurston, T. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structure-function analyses of the bacterial zinc metalloprotease effector protein GtgA uncover key residues required for deactivating NF-kappa B. Authors: Jennings, E. / Esposito, D. / Rittinger, K. / Thurston, T.L.M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ggr.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ggr.ent.gz | 180.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ggr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ggr_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 6ggr_full_validation.pdf.gz | 438.8 KB | Display | |
Data in XML | 6ggr_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6ggr_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/6ggr ftp://data.pdbj.org/pub/pdb/validation_reports/gg/6ggr | HTTPS FTP |
-Related structure data
Related structure data | 6ggoC 2ramS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19316.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rela, Nfkb3 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q04207 | ||
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#2: Protein | Mass: 24098.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria) Gene: gtgA, STM14_1166 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0F6AZI6 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Crystallyzation conditions: 0.1 M Tris pH 8.3, 0.5 M LiCl and 32.5% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.097→55.93 Å / Num. obs: 22948 / % possible obs: 99.03 % / Redundancy: 31.1 % / Rmerge(I) obs: 0.1894 / Rpim(I) all: 0.03482 / Rrim(I) all: 0.1927 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.097→2.172 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RAM Resolution: 2.097→55.93 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.097→55.93 Å
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Refine LS restraints |
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LS refinement shell |
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