2dcu: Difference between revisions

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-[[Image:2dcu.png|left|200px]]
-{{STRUCTURE_2dcu|  PDB=2dcu  |  SCENE=  }}
+==Crystal structure of translation initiation factor aIF2betagamma heterodimer with GDP==
+<StructureSection load='2dcu' size='340' side='right'caption='[[2dcu]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2dcu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DCU FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2dcu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dcu OCA], [https://pdbe.org/2dcu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dcu RCSB], [https://www.ebi.ac.uk/pdbsum/2dcu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dcu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IF2G_PYRFU IF2G_PYRFU] eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA (By similarity).
+== 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/dc/2dcu_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2dcu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Archaeal/eukaryotic initiation factor 2 (a/eIF2) consists of alpha-, beta-, and gamma-subunits and delivers initiator methionine tRNA (Met-tRNA(i)) to a small ribosomal subunit in a GTP-dependent manner. The structures of the aIF2betagamma (archaeal initiation factor 2 betagamma) heterodimeric complex in the apo and GDP forms were analyzed at 2.8- and 3.4-A resolution, respectively. The results showed that the N-terminal helix and the central helix-turn-helix domain of the beta-subunit bind to the G domain of the gamma-subunit but are distant from domains 2 and 3, to which the alpha-subunit and Met-tRNA(i) bind. This result is consistent with most of the previous analyses of eukaryotic factors, and thus indicates that the binding mode is essentially conserved among a/eIF2. Comparison with the uncomplexed structure showed significant differences between the two forms of the beta-subunit, particularly the C-terminal zinc-binding domain, which does not interact with the gamma-subunit and was suggested previously to be involved in GTP hydrolysis. Furthermore, the switch 1 region in the gamma-subunit, which is shown to be responsible for Met-tRNA(i) binding by mutational analysis, is moved away from the nucleotide through the interaction with highly conserved R87 in the beta-subunit. These results implicate that conformational change of the beta-subunit facilitates GTP hydrolysis by inducing the conformational change of the switch 1 region toward the off state.
-===Crystal structure of translation initiation factor aIF2betagamma heterodimer with GDP===
+Structure of archaeal translational initiation factor 2 betagamma-GDP reveals significant conformational change of the beta-subunit and switch 1 region.,Sokabe M, Yao M, Sakai N, Toya S, Tanaka I Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13016-21. Epub 2006 Aug 21. PMID:16924118<ref>PMID:16924118</ref>
-{{ABSTRACT_PUBMED_16924118}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2dcu" style="background-color:#fffaf0;"></div>
-[[2dcu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCU OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:016924118</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Pyrococcus furiosus]]
+[[Category: Large Structures]]
-[[Category: Sakai, N.]]
+[[Category: Pyrococcus furiosus DSM 3638]]
-[[Category: Sokabe, M.]]
+[[Category: Sakai N]]
-[[Category: Tanaka, I.]]
+[[Category: Sokabe M]]
-[[Category: Toya, S.]]
+[[Category: Tanaka I]]
-[[Category: Yao, M.]]
+[[Category: Toya S]]
-[[Category: Protein complex]]
+[[Category: Yao M]]
-[[Category: Translation]]