1tr4: Difference between revisions

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-{{Seed}}
-[[Image:1tr4.png|left|200px]]
-<!--
+==Solution structure of human oncogenic protein gankyrin==
-The line below this paragraph, containing "STRUCTURE_1tr4", creates the "Structure Box" on the page.
+<StructureSection load='1tr4' size='340' side='right'caption='[[1tr4]]' 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'>[[1tr4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TR4 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">Solution NMR</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=1tr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tr4 OCA], [https://pdbe.org/1tr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tr4 RCSB], [https://www.ebi.ac.uk/pdbsum/1tr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tr4 ProSAT]</span></td></tr>
-{{STRUCTURE_1tr4|  PDB=1tr4  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PSD10_HUMAN PSD10_HUMAN] Acts as a chaperone during the assembly of the 26S proteasome, specifically of the PA700/19S regulatory complex (RC). In the initial step of the base subcomplex assembly is part of an intermediate PSMD10:PSMC4:PSMC5:PAAF1 module which probably assembles with a PSMD5:PSMC2:PSMC1:PSMD2 module. Independently of the proteasome, regulates EGF-induced AKT activation through inhibition of the RHOA/ROCK/PTEN pahway, leading to prolonged AKT activation. Plays an important role in RAS-induced tumorigenesis.<ref>PMID:10613832</ref> <ref>PMID:11900540</ref> <ref>PMID:11779854</ref> <ref>PMID:16023600</ref> <ref>PMID:18040287</ref> <ref>PMID:19490896</ref> <ref>PMID:19729910</ref> <ref>PMID:20628200</ref>   Acts as an proto-oncoprotein by being involved in negative regulation of tumor suppressors RB1 and p53/TP53. Overexpression is leading to phosphorylation of RB1 and proteasomal degradation of RB1. Regulates CDK4-mediated phosphorylation of RB1 by competing with CDKN2A for binding with CDK4. Facilitates binding of MDM2 to p53/TP53 and the mono- and polyubiquitination of p53/TP53 by MDM2 suggesting a function in targeting the TP53:MDM2 complex to the 26S proteasome. Involved in p53-independent apoptosis. Involved in regulation of NF-kappa-B by retaining it in the cytoplasm. Binds to the NF-kappa-B component RELA and accelerates its XPO1/CRM1-mediated nuclear export.<ref>PMID:10613832</ref> <ref>PMID:11900540</ref> <ref>PMID:11779854</ref> <ref>PMID:16023600</ref> <ref>PMID:18040287</ref> <ref>PMID:19490896</ref> <ref>PMID:19729910</ref> <ref>PMID:20628200</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/tr/1tr4_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=1tr4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human gankyrin (226 residues, 24.4 kDa) is a liver oncoprotein that plays an important role in the development of human hepatocellular carcinomas. In this paper, its solution structure is reported, which is the largest ankyrin protein ever determined by NMR. The highly degenerate primary sequences of the seven ankyrin repeats presented a major challenge, which was overcome by combined use of TROSY experiments, perdeuterated samples, isotope-filtered NMR experiments, and residual dipolar couplings. The final structure was of high quality, with atomic rmsds for the backbone (N, C', and C(alpha)) and all heavy atoms (residues 4-224) of 0.69 +/- 0.09 and 1.04 +/- 0.09 A, respectively. Detailed analyses of NMR data suggested that the conserved TPLH motifs play important structural roles in stabilizing the repeating ankyrin scaffold. Gankyrin is conformationally more stable than the tumor suppressor p16(INK4A), possibly due to the structural roles of conserved residues evidenced by slowly exchanging backbone amides as well as hydrogen bonding networks involving labile side chain protons. Structural comparison with p16(INK4A) identified several residues of gankyrin that are potentially important for CDK4 binding, whereas observation of the thiol proton of C180 indicated a well-structured Rb-binding site in the helical region of the sixth ankyrin repeat. Interestingly, the CDK4-binding site and Rb-binding site located in N- and C-terminal regions, respectively, are separated by comparatively more stable ankyrin repeats and highly condensed positive surface charge. These results and analyses will shed light on the structural basis of the function of human gankyrin.
-===Solution structure of human oncogenic protein gankyrin===
+Solution structure of the human oncogenic protein gankyrin containing seven ankyrin repeats and analysis of its structure--function relationship.,Yuan C, Li J, Mahajan A, Poi MJ, Byeon IJ, Tsai MD Biochemistry. 2004 Sep 28;43(38):12152-61. PMID:15379554<ref>PMID:15379554</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1tr4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15379554}}, adds the Publication Abstract to the page
+*[[Ankyrin 3D structures|Ankyrin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15379554 is the PubMed ID number.
+*[[Proteasome 3D structures|Proteasome 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_15379554}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-TR4 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TR4 OCA].
-==Reference==
-<ref group="xtra">PMID:15379554</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Byeon, I J.]]
+[[Category: Large Structures]]
-[[Category: Li, J.]]
+[[Category: Byeon IJ]]
-[[Category: Mahajan, A.]]
+[[Category: Li J]]
-[[Category: Poi, M J.]]
+[[Category: Mahajan A]]
-[[Category: Tsai, M D.]]
+[[Category: Poi MJ]]
-[[Category: Yuan, C.]]
+[[Category: Tsai MD]]
-[[Category: Ankyrin repeat]]
+[[Category: Yuan C]]
-[[Category: Gankyrin]]
-[[Category: Nmr]]
-[[Category: Oncoprotein]]
-[[Category: Protein structure]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:48:00 2009''