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Yorodumi- PDB-9bor: IkappaBzeta ankyrin repeat domain:NF-kappaB p50 homodimer complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bor | ||||||
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Title | IkappaBzeta ankyrin repeat domain:NF-kappaB p50 homodimer complex at 2.0 Angstrom resolution | ||||||
Components |
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Keywords | TRANSCRIPTION / Transcription factor / immunoglobulin-like domain / ankyrin repeat domain / protein-protein complex / NF-kappaB / IkappaB | ||||||
Function / homology | Function and homology information keratinocyte activation / response to cisplatin / transcription preinitiation complex assembly / cellular response to diterpene / cellular response to glucoside / positive regulation of T-helper 17 cell differentiation / Regulated proteolysis of p75NTR / B cell receptor apoptotic signaling pathway / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production ...keratinocyte activation / response to cisplatin / transcription preinitiation complex assembly / cellular response to diterpene / cellular response to glucoside / positive regulation of T-helper 17 cell differentiation / Regulated proteolysis of p75NTR / B cell receptor apoptotic signaling pathway / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / chronic inflammatory response / MAP3K8 (TPL2)-dependent MAPK1/3 activation / T-helper 1 cell differentiation / TRAF6 mediated NF-kB activation / response to Gram-positive bacterium / positive regulation of hyaluronan biosynthetic process / 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 / cellular response to carbohydrate stimulus / antibacterial innate immune response / mammary gland involution / FCERI mediated NF-kB activation / POU domain binding / CLEC7A (Dectin-1) signaling / inflammatory response to wounding / Interleukin-1 signaling / cellular response to peptide / cellular response to interleukin-17 / Downstream TCR signaling / NF-kappaB p50/p65 complex / T cell mediated immunity / plasma cell differentiation / T-helper 17 cell differentiation / CD209 (DC-SIGN) signaling / negative regulation of interleukin-12 production / isotype switching / response to folic acid / cellular response to interleukin-6 / cellular response to dsRNA / actinin binding / cellular response to angiotensin / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / non-canonical NF-kappaB signal transduction / toll-like receptor signaling pathway / positive regulation of miRNA metabolic process / B cell proliferation / cellular response to cytokine stimulus / cellular response to organic cyclic compound / keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / cellular response to interleukin-1 / establishment of skin barrier / lymph node development / canonical NF-kappaB signal transduction / keratinocyte differentiation / JNK cascade / homeostasis of number of cells within a tissue / spleen development / cellular response to transforming growth factor beta stimulus / cellular response to brain-derived neurotrophic factor stimulus / heat shock protein binding / response to muscle stretch / Neutrophil degranulation / response to cytokine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / B cell receptor signaling pathway / mRNA transcription by RNA polymerase II / response to organic cyclic compound / cellular response to virus / cytokine-mediated signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / cytoplasmic ribonucleoprotein granule / positive regulation of inflammatory response / cellular response to nicotine / cellular response to mechanical stimulus / MAPK cascade / sequence-specific double-stranded DNA binding / positive regulation of canonical Wnt signaling pathway / cellular response to tumor necrosis factor / T cell receptor signaling pathway / gene expression / regulation of gene expression / double-stranded DNA binding / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to Gram-negative bacterium / response to oxidative stress / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear speck / chromatin remodeling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å | ||||||
Authors | Rogers, W.E. / Zhu, N. / Huxford, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Genes Dev. / Year: 2024 Title: Structural and biochemical analyses of the nuclear I kappa B zeta protein in complex with the NF-kappa B p50 homodimer. Authors: Zhu, N. / Rogers, W.E. / Heidary, D.K. / Huxford, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bor.cif.gz | 127 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bor.ent.gz | 96 KB | Display | PDB format |
PDBx/mmJSON format | 9bor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bor_validation.pdf.gz | 460.6 KB | Display | wwPDB validaton report |
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Full document | 9bor_full_validation.pdf.gz | 467.1 KB | Display | |
Data in XML | 9bor_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 9bor_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/9bor ftp://data.pdbj.org/pub/pdb/validation_reports/bo/9bor | HTTPS FTP |
-Related structure data
Related structure data | 4trv S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34773.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NFKBIZ, IKBZ, INAP, MAIL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BYH8 | ||||||
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#2: Protein | Mass: 15227.196 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C and N terminus unstable and not modeled / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nfkb1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25799 #3: Chemical | ChemComp-HT3 / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop Details: 20mM acetic acid pH 5.2, 80mM acetic acid pH 5.8, 5.5% PEG 3350, 10mM DTT, 0.5% 1,2,3 heptanetriol PH range: 5.2-5.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.997→50 Å / Num. all: 43896 / Num. obs: 43393 / % possible obs: 98.89 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rsym value: 0.055 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.997→2.041 Å / Mean I/σ(I) obs: 2.097 / Num. unique obs: 2608 / Rsym value: 0.468 / % possible all: 96.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TRV 4trv Resolution: 1.997→43.31 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.997→43.31 Å
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Refine LS restraints |
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LS refinement shell |
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