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Open data
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Basic information
Entry | Database: PDB / ID: 1ikn | ||||||
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Title | IKAPPABALPHA/NF-KAPPAB COMPLEX | ||||||
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![]() | TRANSCRIPTION FACTOR / IKB-NFKB COMPLEX | ||||||
Function / homology | ![]() I-kappaB/NF-kappaB complex / 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 ...I-kappaB/NF-kappaB complex / 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 / cytoplasmic sequestering of NF-kappaB / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / antibacterial innate immune response / TAK1-dependent IKK and NF-kappa-B activation / negative regulation of myeloid cell differentiation / cellular response to carbohydrate stimulus / mammary gland involution / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / positive regulation of chondrocyte differentiation / 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 / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / molecular sequestering activity / negative regulation of interleukin-12 production / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / 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 / cellular response to angiotensin / transcription regulator inhibitor activity / 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 / cellular response to cold / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / negative regulation of cytokine production / toll-like receptor 4 signaling pathway / nuclear localization sequence binding / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of miRNA metabolic process / negative regulation of NF-kappaB transcription factor activity / response to cobalamin / negative regulation of Notch signaling pathway / positive regulation of T cell receptor signaling pathway / response to exogenous dsRNA / non-canonical NF-kappaB signal transduction / phosphate ion binding / cellular response to cytokine stimulus / cellular response to lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to organic cyclic compound / general transcription initiation factor binding / NF-kappaB binding / hair follicle development / positive regulation of vascular endothelial growth factor production / positive regulation of cholesterol efflux / positive regulation of transcription initiation by RNA polymerase II / neuropeptide signaling pathway / canonical NF-kappaB signal transduction / RNA polymerase II core promoter sequence-specific DNA binding / response to amino acid / cellular response to interleukin-1 / lymph node development / negative regulation of canonical NF-kappaB signal transduction / JNK cascade / lipopolysaccharide-mediated signaling pathway / Notch signaling pathway / cellular response to brain-derived neurotrophic factor stimulus / response to cAMP / tumor necrosis factor-mediated signaling pathway / heat shock protein binding / protein sequestering activity / response to muscle stretch / positive regulation of protein metabolic process / positive regulation of interleukin-12 production Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huxford, T. / Huang, D.-B. / Malek, S. / Ghosh, G. | ||||||
![]() | ![]() Title: The crystal structure of the IkappaBalpha/NF-kappaB complex reveals mechanisms of NF-kappaB inactivation. Authors: Huxford, T. / Huang, D.B. / Malek, S. / Ghosh, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.9 KB | Display | ![]() |
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PDB format | ![]() | 104.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.2 KB | Display | ![]() |
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Full document | ![]() | 491.9 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 41.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vkxS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32738.027 Da / Num. of mol.: 1 / Fragment: N-TERMINAL AND DIMERIZATION DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 13929.799 Da / Num. of mol.: 1 / Fragment: N-TERMINAL AND DIMERIZATION DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 26098.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23-24 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 28014 / % possible obs: 91 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.5 / % possible all: 59 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / % possible obs: 91 % / Redundancy: 3.5 % / Num. measured all: 160828 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 59 % / Mean I/σ(I) obs: 2.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1VKX Resolution: 2.3→6 Å / σ(F): 3
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Displacement parameters | Biso mean: 48.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.223 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.3 |