3gut

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[[Image:3gut.jpg|left|200px]]
 
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==Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR==
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The line below this paragraph, containing "STRUCTURE_3gut", creates the "Structure Box" on the page.
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<StructureSection load='3gut' size='340' side='right'caption='[[3gut]], [[Resolution|resolution]] 3.59&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3gut]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus Human immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GUT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GUT FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.59&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gut OCA], [https://pdbe.org/3gut PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gut RCSB], [https://www.ebi.ac.uk/pdbsum/3gut PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gut ProSAT]</span></td></tr>
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{{STRUCTURE_3gut| PDB=3gut | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TF65_HUMAN TF65_HUMAN] 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. 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:10928981</ref> <ref>PMID:12748188</ref> <ref>PMID:17000776</ref> <ref>PMID:17620405</ref> <ref>PMID:19058135</ref> <ref>PMID:20547752</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gu/3gut_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3gut ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The activation and latency of human immunodeficiency virus type 1 (HIV-1) are tightly controlled by the transcriptional activity of its long terminal repeat (LTR) region. The LTR is regulated by viral proteins as well as host factors, including the nuclear factor kappaB (NF-kappaB) that becomes activated in virus-infected cells. The two tandem NF-kappaB sites of the LTR are among the most highly conserved sequence elements of the HIV-1 genome. Puzzlingly, these sites are arranged in a manner that seems to preclude simultaneous binding of both sites by NF-kappaB, although previous biochemical work suggests otherwise. Here, we have determined the crystal structure of p50:RelA bound to the tandem kappaB element of the HIV-1 LTR as a dimeric dimer, providing direct structural evidence that NF-kappaB can occupy both sites simultaneously. The two p50:RelA dimers bind the adjacent kappaB sites and interact through a protein contact that is accommodated by DNA bending. The two dimers clamp DNA from opposite faces of the double helix and form a topological trap of the bound DNA. Consistent with these structural features, our biochemical analyses indicate that p50:RelA binds the HIV-1 LTR tandem kappaB sites with an apparent anti-cooperativity but enhanced kinetic stability. The slow on and off rates we observe may be relevant to viral latency because viral activation requires sustained NF-kappaB activation. Furthermore, our work demonstrates that the specific arrangement of the two kappaB sites on the HIV-1 LTR can modulate the assembly kinetics of the higher-order NF-kappaB complex on the viral promoter. This phenomenon is unlikely restricted to the HIV-1 LTR but probably represents a general mechanism for the function of composite DNA elements in transcription.
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===Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR===
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Structural basis of HIV-1 activation by NF-kappaB--a higher-order complex of p50:RelA bound to the HIV-1 LTR.,Stroud JC, Oltman A, Han A, Bates DL, Chen L J Mol Biol. 2009 Oct 16;393(1):98-112. Epub 2009 Aug 14. PMID:19683540<ref>PMID:19683540</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3gut" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19683540}}, adds the Publication Abstract to the page
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*[[NF-kB|NF-kB]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19683540 is the PubMed ID number.
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== References ==
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{{ABSTRACT_PUBMED_19683540}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3GUT is a 12 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus Human immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GUT OCA].
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==Reference==
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<ref group="xtra">PMID:19683540</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Human immunodeficiency virus]]
[[Category: Human immunodeficiency virus]]
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[[Category: Bates, D L.]]
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[[Category: Large Structures]]
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[[Category: Chen, L.]]
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[[Category: Bates DL]]
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[[Category: Han, A.]]
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[[Category: Chen L]]
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[[Category: Oltman, A J.]]
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[[Category: Han A]]
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[[Category: Stroud, J C.]]
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[[Category: Oltman AJ]]
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[[Category: Acetylation]]
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[[Category: Stroud JC]]
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[[Category: Activator]]
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[[Category: Alternative splicing]]
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[[Category: Ank repeat]]
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[[Category: Apoptosis]]
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[[Category: Cytoplasm]]
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[[Category: Dna-binding]]
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[[Category: Ig fold]]
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[[Category: Multiprotein assembly]]
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[[Category: Nucleus]]
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[[Category: Phosphoprotein]]
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[[Category: Polymorphism]]
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[[Category: Protein-dna complex]]
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[[Category: Pseudocontinuous helix]]
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[[Category: Rel family]]
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[[Category: S-nitrosylation]]
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[[Category: Transcription]]
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[[Category: Transcription regulation]]
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[[Category: Transcription/dna complex]]
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[[Category: Ubl conjugation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 9 09:20:47 2009''
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Current revision

Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR

PDB ID 3gut

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