+Open data
-Basic information
Entry | Database: PDB / ID: 1oy3 | ||||||
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Title | CRYSTAL STRUCTURE OF AN IKBBETA/NF-KB P65 HOMODIMER COMPLEX | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Protein-protein complex / Transcription factors / Nuclear localization | ||||||
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 / regulation of 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 Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Malek, S. / Huang, D.B. / Huxford, T. / Ghosh, S. / Ghosh, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: X-ray crystal structure of an IkappaBbeta x NF-kappaB p65 homodimer complex. Authors: Malek, S. / Huang, D.B. / Huxford, T. / Ghosh, S. / Ghosh, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oy3.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oy3.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 1oy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oy3_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 1oy3_full_validation.pdf.gz | 464.7 KB | Display | |
Data in XML | 1oy3_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 1oy3_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/1oy3 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/1oy3 | HTTPS FTP |
-Related structure data
Related structure data | 1k3zSC 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: 15743.802 Da / Num. of mol.: 2 / Fragment: p65 dimerization domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: RELA OR NFKB3 / Plasmid: PET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q04207 #2: Protein | | Mass: 30327.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pet29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q60778 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG 8000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 29193 / % possible obs: 78.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2 / Num. unique all: 2768 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K3Z Resolution: 2.05→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 44.5406 Å2 / ksol: 0.356903 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.1 Å
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