+Open data
-Basic information
Entry | Database: PDB / ID: 9bdw | ||||||
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Title | NF-kappaB RelA homo-dimer bound to GC-centric kappaB DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / RelA / kappaB DNA / Promoter / Transcription / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information 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 / TRAF6 mediated NF-kB activation / 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 ...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 / TRAF6 mediated NF-kB activation / 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 / positive regulation of chondrocyte differentiation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / acetaldehyde metabolic process / prolactin signaling pathway / Downstream TCR signaling / NF-kappaB p50/p65 complex / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / 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 / actinin binding / cellular response to angiotensin / NF-kappaB complex / response to UV-B / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / non-canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of T cell receptor signaling pathway / response to cobalamin / phosphate ion binding / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / NF-kappaB binding / hair follicle development / positive regulation of vascular endothelial growth factor production / neuropeptide signaling pathway / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of interleukin-12 production / negative regulation of angiogenesis / negative regulation of miRNA transcription / liver development / positive regulation of interleukin-1 beta production / response to cytokine / positive regulation of interleukin-8 production / response to ischemia / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / peptide binding / response to bacterium / protein catabolic process / response to insulin / negative regulation of protein catabolic process / chromatin DNA binding / transcription coactivator binding / defense response / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / histone deacetylase binding / cellular response to hydrogen peroxide / cellular response to nicotine / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / chromatin organization / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / double-stranded DNA binding / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / DNA-templated transcription Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Biswas, T. / Shahabi, S. / Tsodikov, O.V. / Huang, D. / Ghosh, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA. Authors: Li, T. / Shahabi, S. / Biswas, T. / Tsodikov, O.V. / Pan, W. / Huang, D.B. / Wang, V.Y. / Wang, Y. / Ghosh, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bdw.cif.gz | 306.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bdw.ent.gz | 240.3 KB | Display | PDB format |
PDBx/mmJSON format | 9bdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bdw_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 9bdw_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 9bdw_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 9bdw_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/9bdw ftp://data.pdbj.org/pub/pdb/validation_reports/bd/9bdw | HTTPS FTP |
-Related structure data
Related structure data | 9bduC 9bdvC 9bdxC 9bdyC 9bdzC 9be0C 9be1C 2ramS S: Starting model for refinement C: citing same article (ref.) |
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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
-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 5884.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#3: DNA chain | Mass: 5764.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 32869.223 Da / Num. of mol.: 2 / Fragment: residues 19-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rela, Nfkb3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04207 #5: Sugar | ChemComp-BOG / | |
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-Non-polymers , 2 types, 569 molecules
#4: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, MES, Spermine, beta-octylglucoside |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→30 Å / Num. obs: 60489 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.987 / Χ2: 0.082 / Net I/σ(I): 9.6 / Num. measured all: 409360 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RAM Resolution: 1.87→29.82 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.356 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.033 Å2
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Refinement step | Cycle: 1 / Resolution: 1.87→29.82 Å
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Refine LS restraints |
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