1qvf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:05, 16 August 2023) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1qvf.png|left|200px]]
 
-
<!--
+
==Structure of a deacylated tRNA minihelix bound to the E site of the large ribosomal subunit of Haloarcula marismortui==
-
The line below this paragraph, containing "STRUCTURE_1qvf", creates the "Structure Box" on the page.
+
<StructureSection load='1qvf' size='340' side='right'caption='[[1qvf]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1qvf]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QVF FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-
{{STRUCTURE_1qvf| PDB=1qvf | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvf OCA], [https://pdbe.org/1qvf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qvf RCSB], [https://www.ebi.ac.uk/pdbsum/1qvf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qvf ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A]
 +
== 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/qv/1qvf_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=1qvf ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
During translation, tRNAs cycle through three binding sites on the ribosome: the A, the P, and the E sites. We have determined the structures of complexes between the Haloarcula marismortui large ribosomal subunit and two different E site substrates: a deacylated tRNA acceptor stem minihelix and a CCA-acceptor end. Both of these tRNA mimics contain analogs of adenosine 76, the component responsible for a large proportion of E site binding affinity. They bind in the center of the loop-extension of protein L44e, and make specific contacts with both L44e and 23S rRNA including bases that are conserved in all three kingdoms of life. These contacts are consistent with the footprinting, protection, and cross-linking data that have identified the E site biochemically. These structures explain the specificity of the E site for deacylated tRNAs, as it is too small to accommodate any relevant aminoacyl-tRNA. The orientation of the minihelix suggests that it may mimic the P/E hybrid state. It appears that the E site on the 50S subunit was formed by only RNA in the last common ancestor of the three kingdoms, since the proteins at the E sites of H. marismortui and Deinucoccus radiodurans large subunits are not homologous.
-
===Structure of a deacylated tRNA minihelix bound to the E site of the large ribosomal subunit of Haloarcula marismortui===
+
Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit.,Schmeing TM, Moore PB, Steitz TA RNA. 2003 Nov;9(11):1345-52. PMID:14561884<ref>PMID:14561884</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_14561884}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1qvf" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 14561884 is the PubMed ID number.
+
-
-->
+
-
{{ABSTRACT_PUBMED_14561884}}
+
-
 
+
-
==About this Structure==
+
-
[[1qvf]] is a 30 chain structure of [[Ribosomal protein L10]], [[Ribosomal protein L2]], [[Ribosomal protein L3]], [[Ribosomal protein L5]], [[Ribosomal protein L6]] and [[Ribosomal protein L7]] with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVF OCA].
+
==See Also==
==See Also==
-
*[[Ribosomal protein L10]]
+
*[[Ribosome 3D structures|Ribosome 3D structures]]
-
*[[Ribosomal protein L2]]
+
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-
*[[Ribosomal protein L3]]
+
== References ==
-
*[[Ribosomal protein L5]]
+
<references/>
-
*[[Ribosomal protein L6]]
+
__TOC__
-
*[[Ribosomal protein L7]]
+
</StructureSection>
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:14561884</ref><references group="xtra"/>
+
[[Category: Haloarcula marismortui]]
[[Category: Haloarcula marismortui]]
-
[[Category: Moore, P B.]]
+
[[Category: Large Structures]]
-
[[Category: Schmeing, T M.]]
+
[[Category: Synthetic construct]]
-
[[Category: Steitz, T A.]]
+
[[Category: Moore PB]]
-
[[Category: Protein-protein complex]]
+
[[Category: Schmeing TM]]
-
[[Category: Protein-rna complex]]
+
[[Category: Steitz TA]]
-
[[Category: Ribosome 50]]
+
-
[[Category: Rna-rna complex]]
+

Current revision

Structure of a deacylated tRNA minihelix bound to the E site of the large ribosomal subunit of Haloarcula marismortui

PDB ID 1qvf

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1qvf"
Personal tools