+Open data
-Basic information
Entry | Database: PDB / ID: 1k3z | ||||||
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Title | X-ray crystal structure of the IkBb/NF-kB p65 homodimer complex | ||||||
Components |
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Keywords | TRANSCRIPTION / 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 / positive regulation of chondrocyte differentiation / CLEC7A (Dectin-1) signaling / 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 / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / NF-kappaB complex / response to UV-B / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / 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 / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / 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 / response to progesterone / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / peptide binding / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA 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 / cellular response to hydrogen peroxide / histone deacetylase binding / positive regulation of miRNA transcription / cellular response to nicotine / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / cellular response to tumor necrosis factor / chromatin organization / 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 / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Shiva, M. / Huang, D.B. / Chen, Y. / 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 | 1k3z.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k3z.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/1k3z ftp://data.pdbj.org/pub/pdb/validation_reports/k3/1k3z | HTTPS FTP |
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-Related structure data
Related structure data | 1oy3C 1iknS 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) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q04207 #2: Protein | | Mass: 30537.604 Da / Num. of mol.: 1 / Mutation: S312E, S313E, S314E, S316E, S318E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET11a / 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 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.03 % | ||||||||||||||||||
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Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 15, 2000 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 16126 / Num. obs: 13724 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 3 / Num. unique all: 1430 / % possible all: 72 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 16126 / % possible obs: 93 % / Num. measured all: 110726 |
Reflection shell | *PLUS % possible obs: 72 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IkBalpha/p65dd (pdb entry 1ikn) Resolution: 2.5→30 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.57 Å
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Refinement | *PLUS Highest resolution: 2.5 Å / Num. reflection obs: 15382 / % reflection Rfree: 5 % / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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