View source for 5u01


==Cooperative DNA binding by two RelA dimers==
<StructureSection load='5u01' size='340' side='right'caption='[[5u01]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5u01]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthesium Synthesium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U01 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5u01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u01 OCA], [https://pdbe.org/5u01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u01 RCSB], [https://www.ebi.ac.uk/pdbsum/5u01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u01 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TF65_MOUSE TF65_MOUSE] NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. NF-kappa-B heterodimeric p65-p50 and p65-c-Rel complexes are transcriptional activators. The NF-kappa-B p65-p65 complex appears to be involved in invasin-mediated activation of IL-8 expression (By similarity). The inhibitory effect of I-kappa-B upon NF-kappa-B the cytoplasm is exerted primarily through the interaction with p65. p65 shows a weak DNA-binding site which could contribute directly to DNA binding in the NF-kappa-B complex. Associates with chromatin at the NF-kappa-B promoter region via association with DDX1.<ref>PMID:21131967</ref> <ref>PMID:22244329</ref> 
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== Publication Abstract from PubMed ==
The nuclear factor kappa B (NF-kappaB) transcription factor family regulates genes involved in cell proliferation and inflammation. The promoters of these genes often contain NF-kappaB binding sites (kappaB sites) arranged in tandem. How NF-kappaB activates transcription through these multiple sites is incompletely understood. We report here an X-ray crystal structure of homodimers comprising the RelA DNA binding domain containing the Rel homology region (RHR) in NF-kappaB bound to an E-selectin promoter fragment with tandem kappaB sites. This structure revealed that two dimers bind asymmetrically to the symmetrically arranged kappaB sites at which multiple cognate contacts between one dimer to the corresponding DNA are broken. Since simultaneous RelA RHR dimer binding to tandem sites in solution was anti-cooperative, we inferred that asymmetric RelA RHR binding with fewer contacts likely indicates a dissociative binding mode. We found that both kappaB sites are essential for reporter gene activation by full-length RelA homodimer, suggesting that dimers facilitate DNA binding to each other even though their stable co-occupation is not promoted. Promoter variants with altered spacing and orientation of tandem kappaB sites displayed unexpected reporter activities that were not explained by solution-binding pattern of RelA RHR. Remarkably, full-length RelA bound all DNAs with a weaker affinity and specificity. Moreover, the transactivation domain (AD) played a negative role in DNA binding. These observations suggest that other nuclear factors influence full-length RelA binding to DNA by neutralizing AD negative effect. We propose that DNA binding by NF-kappaB dimers is highly complex and modulated by facilitated association-dissociation processes.

DNA-binding affinity and transcriptional activity of the RelA homodimer of nuclear factor kappa B are not correlated.,Mulero MC, Huang DB, Nguyen HT, Wang V, Li Y, Biswas T, Ghosh G J Biol Chem. 2017 Sep 21. pii: jbc.M117.813980. doi: 10.1074/jbc.M117.813980. PMID:28935669<ref>PMID:28935669</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Synthesium]]
[[Category: Ghosh G]]
[[Category: Huang D]]