3deg: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 3: / Line 3: @@
 <SX load='3deg' size='340' side='right' viewer='molstar' caption='[[3deg]], [[Resolution|resolution]] 10.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3deg]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DEG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3deg]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DEG FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 10.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lepA, b2569, JW2553 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</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=3deg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3deg OCA], [https://pdbe.org/3deg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3deg RCSB], [https://www.ebi.ac.uk/pdbsum/3deg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3deg ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LEPA_ECOLI LEPA_ECOLI] Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner.<ref>PMID:17110332</ref> <ref>PMID:20045415</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 18: / Line 20: @@
 </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=3deg ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-EF4 (LepA) is an almost universally conserved translational GTPase in eubacteria. It seems to be essential under environmental stress conditions and has previously been shown to back-translocate the tRNAs on the ribosome, thereby reverting the canonical translocation reaction. In the current work, EF4 was directly visualized in the process of back-translocating tRNAs by single-particle cryo-EM. Using flexible fitting methods, we built a model of ribosome-bound EF4 based on the cryo-EM map and a recently published unbound EF4 X-ray structure. The cryo-EM map establishes EF4 as a noncanonical elongation factor that interacts not only with the elongating ribosome, but also with the back-translocated tRNA in the A-site region, which is present in a previously unseen, intermediate state and deviates markedly from the position of a canonical A-tRNA. Our results, therefore, provide insight into the underlying structural principles governing back-translocation.
-A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.,Connell SR, Topf M, Qin Y, Wilson DN, Mielke T, Fucini P, Nierhaus KH, Spahn CM Nat Struct Mol Biol. 2008 Sep;15(9):910-5. PMID:19172743<ref>PMID:19172743</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3deg" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 32: / Line 25: @@
 *[[Escherichia coli LepA%2C the ribosomal back translocase|Escherichia coli LepA%2C the ribosomal back translocase]]
 *[[GTP-binding protein 3D structures|GTP-binding protein 3D structures]]
-*[[Ribosomal protein L11|Ribosomal protein L11]]
+*[[Ribosomal protein L11 3D structures|Ribosomal protein L11 3D structures]]
 *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 == References ==
@@ Line 38: / Line 31: @@
 __TOC__
 </SX>
-[[Category: Ecoli]]
 [[Category: Escherichia coli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Connell, S R]]
+[[Category: Connell SR]]
-[[Category: Fucini, P]]
+[[Category: Fucini P]]
-[[Category: Mielke, T]]
+[[Category: Mielke T]]
-[[Category: Nierhaus, K H]]
+[[Category: Nierhaus KH]]
-[[Category: Qin, Y]]
+[[Category: Qin Y]]
-[[Category: Spahn, C M.T]]
+[[Category: Spahn CMT]]
-[[Category: Topf, M]]
+[[Category: Topf M]]
-[[Category: Wilson, D N]]
+[[Category: Wilson DN]]
-[[Category: Antibiotic resistance]]
-[[Category: Ef4]]
-[[Category: Gtp-binding]]
-[[Category: Lepa]]
-[[Category: Membrane]]
-[[Category: Methylation]]
-[[Category: Nucleotide-binding]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome]]
-[[Category: Rna-binding]]
-[[Category: Rrna-binding]]
-[[Category: Translation]]
-[[Category: Trna-binding]]