1dar: Difference between revisions

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-[[Image:1dar.gif|left|200px]]
- {{Structure
+==ELONGATION FACTOR G IN COMPLEX WITH GDP==
-|PDB= 1dar |SIZE=350|CAPTION= <scene name='initialview01'>1dar</scene>, resolution 2.4&Aring;
+<StructureSection load='1dar' size='340' side='right'caption='[[1dar]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=GDP:GUANOSINE-5'-DIPHOSPHATE'>GDP</scene>
+<table><tr><td colspan='2'>[[1dar]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. The September 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Elongation Factors''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_9 10.2210/rcsb_pdb/mom_2006_9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DAR FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-|GENE=
+<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></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=1dar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dar OCA], [https://pdbe.org/1dar PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dar RCSB], [https://www.ebi.ac.uk/pdbsum/1dar PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dar ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/EFG_THET8 EFG_THET8] Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome.
+== 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/da/1dar_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=1dar ConSurf].
+<div style="clear:both"></div>
-'''ELONGATION FACTOR G IN COMPLEX WITH GDP'''
+==See Also==
+*[[Elongation factor 3D structures|Elongation factor 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-BACKGROUND: Elongation factor G (EF-G) catalyzes the translocation step of translation. During translocation EF-G passes through four main conformational states: the GDP complex, the nucleotide-free state, the GTP complex, and the GTPase conformation. The first two of these conformations have been previously investigated by crystallographic methods. RESULTS: The structure of EF-G-GDP has been refined at 2.4 A resolution. Comparison with the nucleotide-free structure reveals that, upon GDP release, the phosphate-binding loop (P-loop) adopts a closed conformation. This affects the position of helix CG, the switch II loop and domains II, IV and V. Asp83 has a conformation similar to the conformation of the corresponding residue in the EF-Tu/EF-Ts complex. The magnesium ion is absent in EF-G-GDP. CONCLUSIONS: The results illustrate that conformational changes in the P-loop can be transmitted to other parts of the structure. A comparison of the structures of EF-G and EF-Tu suggests that EF-G, like EF-Tu, undergoes a transition with domain rearrangements. The conformation of EF-G-GDP around the nucleotide-binding site may be related to the mechanism of nucleotide exchange.
-==About this Structure==
-DAR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The following page contains interesting information on the relation of 1DAR with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb81_1.html Elongation Factors]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DAR OCA].
-==Reference==
-The structure of elongation factor G in complex with GDP: conformational flexibility and nucleotide exchange., al-Karadaghi S, Aevarsson A, Garber M, Zheltonosova J, Liljas A, Structure. 1996 May 15;4(5):555-65. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8736554 8736554]
 [[Category: Elongation Factors]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Thermus thermophilus]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Aevarsson, A.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Al-Karadaghi, S.]]
+[[Category: Aevarsson A]]
-[[Category: Garber, M.]]
+[[Category: Al-Karadaghi S]]
-[[Category: Liljas, A.]]
+[[Category: Garber M]]
-[[Category: Zheltonosova, J.]]
+[[Category: Liljas A]]
-[[Category: GDP]]
+[[Category: Zheltonosova J]]
-[[Category: ribosomal translocase]]
-[[Category: translational gtpase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:35:29 2008''