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Yorodumi- PDB-8tkm: Murine NF-kappaB p50 Rel Homology Region homodimer in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 8tkm | ||||||
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Title | Murine NF-kappaB p50 Rel Homology Region homodimer in complex with 17-mer kappaB DNA from human interleukin-6 (IL-6) promoter | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / DNA / NF-kappaB / p50 / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information cellular response to diterpene / cellular response to glucoside / 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 ...cellular response to diterpene / cellular response to glucoside / 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 / antibacterial innate immune response / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / mammary gland involution / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / cellular response to peptide / Downstream TCR signaling / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / CD209 (DC-SIGN) signaling / negative regulation of interleukin-12 production / cellular response to dsRNA / cellular response to interleukin-6 / actinin binding / cellular response to angiotensin / negative regulation of cytokine production / positive regulation of miRNA metabolic process / non-canonical NF-kappaB signal transduction / cellular response to cytokine stimulus / cellular response to organic cyclic compound / positive regulation of transcription initiation by RNA polymerase II / canonical NF-kappaB signal transduction / lymph node development / cellular response to interleukin-1 / JNK cascade / cellular response to brain-derived neurotrophic factor stimulus / heat shock protein binding / response to muscle stretch / Neutrophil degranulation / protein sequestering activity / response to cytokine / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / response to organic cyclic compound / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / cellular response to mechanical stimulus / cellular response to nicotine / positive regulation of canonical Wnt signaling pathway / MAPK cascade / sequence-specific double-stranded DNA binding / gene expression / cellular response to tumor necrosis factor / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to oxidative stress / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / chromatin binding / chromatin / protein-containing complex binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Zhu, N. / Mealka, M. / Mitchel, S. / Rogers, W.E. / Huxford, T. | ||||||
Funding support | 1items
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Citation | Journal: Biomolecules / Year: 2023 Title: X-ray Crystallographic Study of Preferred Spacing by the NF-kappa B p50 Homodimer on kappa B DNA. Authors: Zhu, N. / Mealka, M. / Mitchel, S. / Milani, C. / Acuna, L.M. / Rogers, E. / Lahana, A.N. / Huxford, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tkm.cif.gz | 189.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tkm.ent.gz | 117.7 KB | Display | PDB format |
PDBx/mmJSON format | 8tkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/8tkm ftp://data.pdbj.org/pub/pdb/validation_reports/tk/8tkm | HTTPS FTP |
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-Related structure data
Related structure data | 8tklC 8tknC 1nfkS 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
#1: Protein | Mass: 34924.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nfkb1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25799 #2: DNA chain | | Mass: 5224.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | | Mass: 5189.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 56.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na-Acetate pH 4.9, 16% (w/v) PEG 1500 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.43 Å / Num. obs: 22616 / % possible obs: 99.9 % / Redundancy: 17.5 % / Biso Wilson estimate: 59.41 Å2 / Rsym value: 0.079 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.8→2.92 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2260 / Rsym value: 0.594 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NFK Resolution: 2.8→48.43 Å / SU ML: 0.4339 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.81 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.43 Å
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Refine LS restraints |
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LS refinement shell |
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