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- PDB-7vuq: Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vuq | |||||||||
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Title | Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin kB DNA fragment | |||||||||
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![]() | DNA BINDING PROTEIN/DNA / DNA-protein complex / transcription factor / TRANSCRIPTION / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / germinal center formation / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / Interleukin-1 processing / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation ...follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / germinal center formation / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / Interleukin-1 processing / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / canonical NF-kappaB signal transduction / Purinergic signaling in leishmaniasis infection / spleen development / extracellular matrix organization / response to cytokine / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / TAK1-dependent IKK and NF-kappa-B activation / PKMTs methylate histone lysines / sequence-specific double-stranded DNA binding / rhythmic process / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / 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 / innate immune response / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Meshcheryakov, V.A. / Wang, V.Y.-F. | |||||||||
Funding support | Macao, 2items
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![]() | ![]() Title: Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation. Authors: Pan, W. / Meshcheryakov, V.A. / Li, T. / Wang, Y. / Ghosh, G. / Wang, V.Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.7 KB | Display | ![]() |
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PDB format | ![]() | 115.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.8 KB | Display | ![]() |
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Full document | ![]() | 480.8 KB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cliC ![]() 7vupC ![]() 7w7lC ![]() 1a3qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 43732.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | | Mass: 5581.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #3: DNA chain | | Mass: 5452.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M Sodium malonate, pH 4.0, 50mM CsCl, 2.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→46.48 Å / Num. obs: 18756 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 3.1→3.27 Å / Num. unique obs: 2690 / CC1/2: 0.934 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1a3q Resolution: 3.1→40.003 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.2 / SU B: 33.276 / SU ML: 0.496 / Average fsc free: 0.7887 / Average fsc work: 0.8027 / Cross valid method: FREE R-VALUE / ESU R Free: 0.433 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 131.11 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→40.003 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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