This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2v2t

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:03, 13 December 2023) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2v2t.jpg|left|200px]]
 
-
<!--
+
==X-ray structure of a NF-kB p50-RelB-DNA complex==
-
The line below this paragraph, containing "STRUCTURE_2v2t", creates the "Structure Box" on the page.
+
<StructureSection load='2v2t' size='340' side='right'caption='[[2v2t]], [[Resolution|resolution]] 3.05&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'>[[2v2t]] is a 4 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=2V2T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V2T 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]] 3.05&#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=2v2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v2t OCA], [https://pdbe.org/2v2t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v2t RCSB], [https://www.ebi.ac.uk/pdbsum/2v2t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v2t ProSAT]</span></td></tr>
-
{{STRUCTURE_2v2t| PDB=2v2t | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RELB_MOUSE RELB_MOUSE] NF-kappa-B is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processed 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. 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 RelB-p50 and RelB-p52 complexes are transcriptional activators. RELB neither associates with DNA nor with RELA/p65 or REL. Stimulates promoter activity in the presence of NFKB2/p49 (By similarity). As a member of the NUPR1/RELB/IER3 survival pathway, may allow the development of pancreatic intraepithelial neoplasias.<ref>PMID:22565310</ref>
 +
== 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/v2/2v2t_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=2v2t ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
We describe here the X-ray crystal structure of NF-kappaB p50/RelB heterodimer bound to a kappaB DNA. Although the global modes of subunit association and kappaB DNA recognition are similar to other NF-kappaB/DNA complexes, this complex reveals distinctive features not observed for non-RelB complexes. For example, Lys274 of RelB is removed from the protein-DNA interface whereas the corresponding residues in all other subunits make base-specific contacts. This mode of binding suggests that RelB may allow the recognition of more diverse kappaB sequences. Complementary surfaces on RelB and p50, as revealed by the crystal contacts, are highly suggestive of assembly of multiple p50/RelB heterodimers on tandem kappaB sites in solution. Consistent with this model our in vitro binding experiments reveal optimal assembly of two wild-type p50/RelB heterodimers on tandem HIV kappaB DNA with 2 bp spacing but not by a mutant heterodimer where one of the RelB packing surface is altered. We suggest that multiple NF-kappaB dimers assemble at diverse kappaB promoters through direct interactions utilizing unique protein-protein interaction surfaces.
-
'''X-RAY STRUCTURE OF A NF-KB P50-RELB-DNA COMPLEX'''
+
X-ray structure of a NF-kappaB p50/RelB/DNA complex reveals assembly of multiple dimers on tandem kappaB sites.,Moorthy AK, Huang DB, Wang VY, Vu D, Ghosh G J Mol Biol. 2007 Oct 26;373(3):723-34. Epub 2007 Aug 22. PMID:17869269<ref>PMID:17869269</ref>
-
 
+
-
 
+
-
==Overview==
+
-
We describe here the X-ray crystal structure of NF-kappaB p50/RelB heterodimer bound to a kappaB DNA. Although the global modes of subunit association and kappaB DNA recognition are similar to other NF-kappaB/DNA complexes, this complex reveals distinctive features not observed for non-RelB complexes. For example, Lys274 of RelB is removed from the protein-DNA interface whereas the corresponding residues in all other subunits make base-specific contacts. This mode of binding suggests that RelB may allow the recognition of more diverse kappaB sequences. Complementary surfaces on RelB and p50, as revealed by the crystal contacts, are highly suggestive of assembly of multiple p50/RelB heterodimers on tandem kappaB sites in solution. Consistent with this model our in vitro binding experiments reveal optimal assembly of two wild-type p50/RelB heterodimers on tandem HIV kappaB DNA with 2 bp spacing but not by a mutant heterodimer where one of the RelB packing surface is altered. We suggest that multiple NF-kappaB dimers assemble at diverse kappaB promoters through direct interactions utilizing unique protein-protein interaction surfaces.
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
2V2T is a [[Protein complex]] structure of sequences 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=2V2T OCA].
+
</div>
 +
<div class="pdbe-citations 2v2t" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
X-ray structure of a NF-kappaB p50/RelB/DNA complex reveals assembly of multiple dimers on tandem kappaB sites., Moorthy AK, Huang DB, Wang VY, Vu D, Ghosh G, J Mol Biol. 2007 Oct 26;373(3):723-34. Epub 2007 Aug 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17869269 17869269]
+
*[[NF-kB|NF-kB]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
-
[[Category: Protein complex]]
+
[[Category: Ghosh G]]
-
[[Category: Ghosh, G.]]
+
[[Category: Huang DB]]
-
[[Category: Huang, D B.]]
+
[[Category: Moorthy AK]]
-
[[Category: Moorthy, A K.]]
+
[[Category: Vu D]]
-
[[Category: Vu, D.]]
+
[[Category: Wang VY]]
-
[[Category: Wang, V Y.]]
+
-
[[Category: 4-diphosphocytidyl-2c-methyl-d-erythritol]]
+
-
[[Category: Aquifex aeolicus]]
+
-
[[Category: Atp-binding]]
+
-
[[Category: Isoprene biosynthesis]]
+
-
[[Category: Kinase]]
+
-
[[Category: Non-mevalonate]]
+
-
[[Category: Nucleotide-binding]]
+
-
[[Category: Transcription]]
+
-
[[Category: Transferase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 18:06:52 2008''
+

Current revision

X-ray structure of a NF-kB p50-RelB-DNA complex

PDB ID 2v2t

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2v2t"
Personal tools