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Yorodumi- PDB-7w7l: Structure of NF-kB p52 homodimer bound to 13-mer A/T-centric P-Se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w7l | |||||||||
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Title | Structure of NF-kB p52 homodimer bound to 13-mer A/T-centric P-Selectin kB DNA fragment | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN-DNA/DNA / DNA-protein complex / transcription factor / TRANSCRIPTION / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN-DNA-DNA complex | |||||||||
Function / homology | Function and homology information 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 / NIK-->noncanonical NF-kB signaling / response to cytokine / Dectin-1 mediated noncanonical NF-kB signaling / TAK1-dependent IKK and NF-kappa-B activation / PKMTs methylate histone lysines / rhythmic process / sequence-specific double-stranded DNA binding / 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 / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Meshcheryakov, V.A. / Wang, V.Y.-F. | |||||||||
Funding support | Macao, 2items
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Citation | Journal: Elife / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w7l.cif.gz | 152.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w7l.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 7w7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/7w7l ftp://data.pdbj.org/pub/pdb/validation_reports/w7/7w7l | HTTPS FTP |
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-Related structure data
Related structure data | 7cliC 7vupC 7vuqC 1a3qS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 36739.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NFKB2, LYT10 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q00653 #2: DNA chain | | Mass: 3992.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | | Mass: 3952.573 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: 4.36 Å3/Da / Density % sol: 71.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 50mM MES, pH 6.0, 10mM MgCl2, 10% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å |
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→48.77 Å / Num. obs: 29500 / % possible obs: 100 % / Redundancy: 37.3 % / CC1/2: 0.999 / Net I/σ(I): 18 |
Reflection shell | Resolution: 3→3.16 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4217 / CC1/2: 0.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A3Q Resolution: 3→48.77 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.898 / SU B: 16.908 / SU ML: 0.292 / Cross valid method: FREE R-VALUE / ESU R: 0.617 / ESU R Free: 0.34 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: 116.662 Å2
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Refinement step | Cycle: LAST / Resolution: 3→48.77 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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