1yd8: Difference between revisions

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-[[Image:1yd8.png|left|200px]]
-<!--
+==COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN==
-The line below this paragraph, containing "STRUCTURE_1yd8", creates the "Structure Box" on the page.
+<StructureSection load='1yd8' size='340' side='right'caption='[[1yd8]], [[Resolution|resolution]] 2.80&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'>[[1yd8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD8 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]] 2.8&#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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [https://pdbe.org/1yd8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [https://www.ebi.ac.uk/pdbsum/1yd8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd8 ProSAT]</span></td></tr>
-{{STRUCTURE_1yd8|  PDB=1yd8  |  SCENE=  }}
+</table>
+== Function ==
-===COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN===
+[https://www.uniprot.org/uniprot/UBC_BOVIN UBC_BOVIN] Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
-<!--
+Check<jmol>
-The line below this paragraph, {{ABSTRACT_PUBMED_15701688}}, adds the Publication Abstract to the page
+  <jmolCheckbox>
-(as it appears on PubMed at http://www.pubmed.gov), where 15701688 is the PubMed ID number.
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd8_consurf.spt"</scriptWhenChecked>
--->
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-{{ABSTRACT_PUBMED_15701688}}
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
-==About this Structure==
+</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=1yd8 ConSurf].
-[[1yd8]] is a 4 chain structure of [[Ubiquitin]] with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA].
+<div style="clear:both"></div>
 ==See Also==
-*[[Ubiquitin]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
+__TOC__
-==Reference==
+</StructureSection>
-<ref group="xtra">PMID:15701688</ref><references group="xtra"/>
 [[Category: Bos taurus]]
 [[Category: Homo sapiens]]
-[[Category: Arighi, C N.]]
+[[Category: Large Structures]]
-[[Category: Beach, B M.]]
+[[Category: Arighi CN]]
-[[Category: Bonifacino, J S.]]
+[[Category: Beach BM]]
-[[Category: Hurley, J H.]]
+[[Category: Bonifacino JS]]
-[[Category: Lee, S.]]
+[[Category: Hurley JH]]
-[[Category: Mattera, R.]]
+[[Category: Lee S]]
-[[Category: Prag, G.]]
+[[Category: Mattera R]]
-[[Category: Chromosomal protein]]
+[[Category: Prag G]]
-[[Category: Mono-ubiquitination]]
-[[Category: Post translational modification]]
-[[Category: Protein transport]]
-[[Category: Trafficking]]