+Open data
-Basic information
Entry | Database: PDB / ID: 1ikn | ||||||
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Title | IKAPPABALPHA/NF-KAPPAB COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION FACTOR / IKB-NFKB COMPLEX | ||||||
Function / homology | Function and homology information 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 / cytoplasmic sequestering of NF-kappaB / 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 / negative regulation of myeloid cell differentiation / cellular response to carbohydrate stimulus / antibacterial innate immune response / mammary gland involution / positive regulation of chondrocyte differentiation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / acetaldehyde metabolic process / prolactin signaling pathway / cellular response to interleukin-17 / Downstream TCR signaling / NF-kappaB p50/p65 complex / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / response to cobalamin / positive regulation of Schwann cell differentiation / cellular response to peptide / 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 / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / cellular response to dsRNA / negative regulation of non-canonical NF-kappaB signal transduction / actinin binding / cellular response to angiotensin / transcription regulator inhibitor activity / response to UV-B / negative regulation of macrophage derived foam cell differentiation / NF-kappaB complex / negative regulation of lipid storage / hair follicle development / 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 / positive regulation of miRNA metabolic process / non-canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / nuclear localization sequence binding / positive regulation of cholesterol efflux / negative regulation of NF-kappaB transcription factor activity / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / negative regulation of Notch signaling pathway / positive regulation of T cell receptor signaling pathway / response to exogenous dsRNA / phosphate ion binding / cellular response to cytokine stimulus / cellular response to lipoteichoic acid / response to muramyl dipeptide / TRAF6 mediated NF-kB activation / general transcription initiation factor binding / cellular response to organic cyclic compound / neuropeptide signaling pathway / NF-kappaB binding / cellular response to interleukin-1 / positive regulation of vascular endothelial growth factor production / positive regulation of transcription initiation by RNA polymerase II / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / lymph node development / negative regulation of angiogenesis / canonical NF-kappaB signal transduction / negative regulation of canonical NF-kappaB signal transduction / negative regulation of miRNA transcription / JNK cascade / transcription coregulator activity / lipopolysaccharide-mediated signaling pathway / negative regulation of insulin receptor signaling pathway / Notch signaling pathway / tumor necrosis factor-mediated signaling pathway / response to cAMP / cellular response to brain-derived neurotrophic factor stimulus / heat shock protein binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Huxford, T. / Huang, D.-B. / Malek, S. / Ghosh, G. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ikn.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ikn.ent.gz | 104.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ikn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ikn_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
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Full document | 1ikn_full_validation.pdf.gz | 491.9 KB | Display | |
Data in XML | 1ikn_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 1ikn_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/1ikn ftp://data.pdbj.org/pub/pdb/validation_reports/ik/1ikn | HTTPS FTP |
-Related structure data
Related structure data | 1vkxS S: Starting model for refinement |
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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: 32738.027 Da / Num. of mol.: 1 / Fragment: N-TERMINAL AND DIMERIZATION DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q04207 |
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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.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P25799 |
#3: Protein | Mass: 26098.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAD-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P25963 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.54 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |