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Open data
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Basic information
Entry | Database: PDB / ID: 1nfi | ||||||
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Title | I-KAPPA-B-ALPHA/NF-KAPPA-B COMPLEX | ||||||
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![]() | COMPLEX (TRANSCRIPTION REG/ANK REPEAT) / COMPLEX (TRANSCRIPTION REGULATION-ANK REPEAT) / ANKYRIN REPEAT / COMPLEX (TRANSCRIPTION REG-ANK REPEAT) COMPLEX | ||||||
Function / homology | ![]() negative regulation of calcidiol 1-monooxygenase activity / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / cytoplasmic sequestering of NF-kappaB / antibacterial innate immune response / negative regulation of myeloid cell differentiation / mammary gland involution / acetaldehyde metabolic process ...negative regulation of calcidiol 1-monooxygenase activity / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / cytoplasmic sequestering of NF-kappaB / antibacterial innate immune response / negative regulation of myeloid cell differentiation / mammary gland involution / acetaldehyde metabolic process / prolactin signaling pathway / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / positive regulation of macrophage derived foam cell differentiation / positive regulation of Schwann cell differentiation / positive regulation of lipid storage / cellular response to peptidoglycan / molecular sequestering activity / negative regulation of interleukin-12 production / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / 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 / Interleukin-1 processing / 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 / Regulation of NFE2L2 gene expression / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / negative regulation of protein metabolic process / 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 lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / The NLRP3 inflammasome / general transcription initiation factor binding / Transcriptional Regulation by VENTX / 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 / cellular defense response / Purinergic signaling in leishmaniasis infection / negative regulation of canonical NF-kappaB signal transduction / JNK cascade / lipopolysaccharide-mediated signaling pathway / Notch signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / protein sequestering activity / response to muscle stretch / positive regulation of protein metabolic process / positive regulation of interleukin-12 production / negative regulation of insulin receptor signaling pathway / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / response to interleukin-1 / negative regulation of angiogenesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / : / negative regulation of miRNA transcription / liver development / positive regulation of interleukin-1 beta production / response to cytokine / positive regulation of interleukin-8 production Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jacobs, M.D. / Harrison, S.C. | ||||||
![]() | ![]() Title: Structure of an IkappaBalpha/NF-kappaB complex. Authors: Jacobs, M.D. / Harrison, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249.9 KB | Display | ![]() |
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PDB format | ![]() | 200.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 403.8 KB | Display | ![]() |
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Full document | ![]() | 460 KB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 47.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, 0.003, -0.001), Vector: |
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Components
#1: Protein | Mass: 34547.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 12442.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 23312.512 Da / Num. of mol.: 2 / Fragment: ANKYRIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4, 20 ℃ / 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: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B4 / Detector: CCD |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9879 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 41990 / % possible obs: 92 % / Redundancy: 3.6 % / Biso Wilson estimate: 60.4 Å2 / Rsym value: 0.05 |
Reflection | *PLUS Redundancy: 3.7 % / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 83 % / Rmerge(I) obs: 0.206 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.18 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 39742 / Rfactor obs: 0.222 / Rfactor Rfree: 0.315 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.315 |