5mdv: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
m Protected "5mdv" [edit=sysop:move=sysop]
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
'''Unreleased structure'''


The entry 5mdv is ON HOLD
==Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state)==
<SX load='5mdv' size='340' side='right' viewer='molstar' caption='[[5mdv]], [[Resolution|resolution]] 2.97&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5mdv]] 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=5MDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MDV FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.97&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=8AN:3-AMINO-3-DEOXYADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>8AN</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MEQ:N5-METHYLGLUTAMINE'>MEQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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=5mdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdv OCA], [https://pdbe.org/5mdv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mdv RCSB], [https://www.ebi.ac.uk/pdbsum/5mdv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdv ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine structures of ArfA bound to the ribosome with 3'-truncated mRNA, at resolutions ranging from 3.0 to 3.4 angstroms. ArfA binds within the ribosomal mRNA channel and substitutes for the absent stop codon in the A site by specifically recruiting release factor 2 (RF2), initially in a compact preaccommodated state. A similar conformation of RF2 may occur on stop codons, suggesting a general mechanism for release-factor-mediated translational termination in which a conformational switch leads to peptide release only when the appropriate signal is present in the A site.


Authors:  
Translational termination without a stop codon.,James NR, Brown A, Gordiyenko Y, Ramakrishnan V Science. 2016 Dec 16;354(6318):1437-1440. Epub 2016 Dec 1. PMID:27934701<ref>PMID:27934701</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 5mdv" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
__TOC__
</SX>
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Brown A]]
[[Category: Gordiyenko Y]]
[[Category: James NR]]
[[Category: Ramakrishnan V]]
Retrieved from "https://proteopedia.org/5mdv"