1bfs: Difference between revisions

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-{{Seed}}
-[[Image:1bfs.png|left|200px]]
-<!--
+==STRUCTURE OF NF-KB P50 HOMODIMER BOUND TO A KB SITE==
-The line below this paragraph, containing "STRUCTURE_1bfs", creates the "Structure Box" on the page.
+<StructureSection load='1bfs' size='340' side='right'caption='[[1bfs]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1bfs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BFS FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#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=1bfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfs OCA], [https://pdbe.org/1bfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bfs RCSB], [https://www.ebi.ac.uk/pdbsum/1bfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bfs ProSAT]</span></td></tr>
-{{STRUCTURE_1bfs|  PDB=1bfs  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NFKB1_MOUSE NFKB1_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 RelB-p50 complexes are transcriptional activators. The NF-kappa-B p50-p50 homodimer is a transcriptional repressor, but can act as a transcriptional activator when associated with BCL3. NFKB1 appears to have dual functions such as cytoplasmic retention of attached NF-kappa-B proteins by p105 and generation of p50 by a cotranslational processing. The proteasome-mediated process ensures the production of both p50 and p105 and preserves their independent function, although processing of NFKB1/p105 also appears to occur post-translationally. p50 binds to the kappa-B consensus sequence 5'-GGRNNYYCC-3', located in the enhancer region of genes involved in immune response and acute phase reactions. Plays a role in the regulation of apoptosis. Isoform 5, isoform 6 and isoform 7 act as inhibitors of transactivation of p50 NF-kappa-B subunit, probably by sequestering it in the cytoplasm. Isoform 3 (p98) (but not p84 or p105) acts as a transactivator of NF-kappa-B-regulated gene expression. In a complex with MAP3K8, NFKB1/p105 represses MAP3K8-induced MAPK signaling; active MAP3K8 is released by proteasome-dependent degradation of NFKB1/p105.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bf/1bfs_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bfs ConSurf].
+<div style="clear:both"></div>
-===STRUCTURE OF NF-KB P50 HOMODIMER BOUND TO A KB SITE===
+==See Also==
+*[[NF-kB|NF-kB]]
+__TOC__
-<!--
+</StructureSection>
-The line below this paragraph, {{ABSTRACT_PUBMED_9384558}}, adds the Publication Abstract to the page
+[[Category: Large Structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9384558 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_9384558}}
-==About this Structure==
-BFS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFS OCA].
-==Reference==
-The role of DNA in the mechanism of NFkappaB dimer formation: crystal structures of the dimerization domains of the p50 and p65 subunits., Huang DB, Huxford T, Chen YQ, Ghosh G, Structure. 1997 Nov 15;5(11):1427-36. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9384558 9384558]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Chen YQ]]
-[[Category: Chen, Y Q.]]
+[[Category: Ghosh G]]
-[[Category: Ghosh, G.]]
+[[Category: Huang DB]]
-[[Category: Huang, D B.]]
+[[Category: Huxford T]]
-[[Category: Huxford, T.]]
-[[Category: Dimerization domain]]
-[[Category: Nf-kb]]
-[[Category: Transcription factor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 19:03:44 2008''