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1ml5

From Proteopedia

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[[Image:1ml5.gif|left|200px]]
 
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==Structure of the E. coli ribosomal termination complex with release factor 2==
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The line below this paragraph, containing "STRUCTURE_1ml5", creates the "Structure Box" on the page.
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<SX load='1ml5' size='340' side='right' viewer='molstar' caption='[[1ml5]], [[Resolution|resolution]] 14.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1ml5]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ML5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ML5 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 14&#8491;</td></tr>
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<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>
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{{STRUCTURE_1ml5| PDB=1ml5 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ml5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ml5 OCA], [https://pdbe.org/1ml5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ml5 RCSB], [https://www.ebi.ac.uk/pdbsum/1ml5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ml5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RF2_ECOLI RF2_ECOLI] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.[HAMAP-Rule:MF_00094]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ml/1ml5_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1ml5 ConSurf].
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<div style="clear:both"></div>
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'''Structure of the E. coli ribosomal termination complex with release factor 2'''
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==See Also==
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*[[MHC 3D structures|MHC 3D structures]]
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*[[MHC I 3D structures|MHC I 3D structures]]
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==Overview==
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*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
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Termination of protein synthesis occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide motifs, leading to release of the completed polypeptide chain from its covalent attachment to transfer RNA in the ribosomal peptidyl (P) site. Class I RFs possess a conserved GGQ amino-acid motif that is thought to be involved directly in protein-transfer-RNA bond hydrolysis. Crystal structures of bacterial and eukaryotic class I RFs have been determined, but the mechanism of stop codon recognition and peptidyl-tRNA hydrolysis remains unclear. Here we present the structure of the Escherichia coli ribosome in a post-termination complex with RF2, obtained by single-particle cryo-electron microscopy (cryo-EM). Fitting the known 70S and RF2 structures into the electron density map reveals that RF2 adopts a different conformation on the ribosome when compared with the crystal structure of the isolated protein. The amino-terminal helical domain of RF2 contacts the factor-binding site of the ribosome, the 'SPF' loop of the protein is situated close to the mRNA, and the GGQ-containing domain of RF2 interacts with the peptidyl-transferase centre (PTC). By connecting the ribosomal decoding centre with the PTC, RF2 functionally mimics a tRNA molecule in the A site. Translational termination in eukaryotes is likely to be based on a similar mechanism.
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*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
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__TOC__
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==About this Structure==
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</SX>
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1ML5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ML5 OCA].
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==Reference==
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Structure of the Escherichia coli ribosomal termination complex with release factor 2., Klaholz BP, Pape T, Zavialov AV, Myasnikov AG, Orlova EV, Vestergaard B, Ehrenberg M, van Heel M, Nature. 2003 Jan 2;421(6918):90-4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12511961 12511961]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Ehrenberg, M.]]
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[[Category: Ehrenberg M]]
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[[Category: Heel, M van.]]
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[[Category: Klaholz BP]]
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[[Category: Klaholz, B P.]]
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[[Category: Myasnikov AG]]
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[[Category: Myasnikov, A G.]]
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[[Category: Orlova EV]]
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[[Category: Orlova, E V.]]
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[[Category: Pape T]]
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[[Category: Pape, T.]]
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[[Category: Vestergaard B]]
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[[Category: Vestergaard, B.]]
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[[Category: Zavialov AV]]
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[[Category: Zavialov, A V.]]
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[[Category: Van Heel M]]
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[[Category: Angular reconstitution]]
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[[Category: Cryo-eletron microscopy]]
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[[Category: E. coli]]
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[[Category: Release factor]]
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[[Category: Ribosome]]
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[[Category: Termination of protein synthesis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 01:21:54 2008''
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Current revision

Structure of the E. coli ribosomal termination complex with release factor 2

1ml5, resolution 14.00Å

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