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Yorodumi- PDB-1vkx: CRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO TH... -
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-Basic information
Entry | Database: PDB / ID: 1vkx | ||||||
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Title | CRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO THE IMMUNOGLOBULIN KB DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / NF-KB / HETERODIMER / DNA-BINDING / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information cellular response to diterpene / cellular response to glucoside / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process ...cellular response to diterpene / cellular response to glucoside / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival / PKMTs methylate histone lysines / antibacterial innate immune response / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / mammary gland involution / FCERI mediated NF-kB activation / positive regulation of chondrocyte differentiation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / cellular response to peptide / acetaldehyde metabolic process / Downstream TCR signaling / prolactin signaling pathway / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / negative regulation of interleukin-12 production / ankyrin repeat binding / negative regulation of protein sumoylation / defense response to tumor cell / cellular response to dsRNA / 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 / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of cytokine production / 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 / positive regulation of miRNA metabolic process / response to cobalamin / positive regulation of T cell receptor signaling pathway / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to cytokine stimulus / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / cellular response to organic cyclic compound / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of transcription initiation by RNA polymerase II / positive regulation of vascular endothelial growth factor production / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / cellular response to interleukin-1 / response to amino acid / lymph node development / JNK cascade / cellular response to brain-derived neurotrophic factor stimulus / response to cAMP / tumor necrosis factor-mediated signaling pathway / heat shock protein binding / response to muscle stretch / negative regulation of insulin receptor signaling pathway / Neutrophil degranulation / positive regulation of interleukin-12 production / 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 / transcription coregulator activity / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / response to bacterium / protein catabolic process / response to insulin / response to organic cyclic compound / negative regulation of protein catabolic process / chromatin DNA binding / cellular response to virus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMEN / Resolution: 2.9 Å | ||||||
Authors | Chen, F. / Huang, D.B. / Ghosh, G. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. Authors: Chen, F.E. / Huang, D.B. / Chen, Y.Q. / Ghosh, G. #1: Journal: Nature / Year: 1995 Title: Structure of NF-Kb p50 Homodimer Bound to a Kb Site Authors: Ghosh, G. / Duyne, G.V. / Ghosh, S. / Sigler, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vkx.cif.gz | 141.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vkx.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 1vkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/1vkx ftp://data.pdbj.org/pub/pdb/validation_reports/vk/1vkx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3669.389 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: ACTIVE NF-KAPPA-B IS A HETERODIMER OF AN ABOUT 50 KD DNA-BINDING SUBUNIT AND THE WEAK DNA-BINDING SUBUNIT P65 |
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#2: DNA chain | Mass: 3656.407 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: ACTIVE NF-KAPPA-B IS A HETERODIMER OF AN ABOUT 50 KD DNA-BINDING SUBUNIT AND THE WEAK DNA-BINDING SUBUNIT P65 |
#3: Protein | Mass: 30984.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q04207 |
#4: Protein | Mass: 34924.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P25799 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.99 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 / Details: pH 5.50, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 26430 / % possible obs: 97 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.45 / % possible all: 88 |
Reflection | *PLUS Num. measured all: 88449 |
Reflection shell | *PLUS % possible obs: 88 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMEN Starting model: ONE MONOMER OF P50/DNA COMPLEX AND ONE MONO OF P65/DNA COMPLEX Resolution: 2.9→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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