1q86

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:59, 16 August 2023) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1q86.png|left|200px]]
 
-
{{STRUCTURE_1q86| PDB=1q86 | SCENE= }}
+
==Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit.==
 +
<StructureSection load='1q86' size='340' side='right'caption='[[1q86]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1q86]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q86 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q86 FirstGlance]. <br>
 +
</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&#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>, <scene name='pdbligand=PHA:PHENYLALANINAL'>PHA</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=1q86 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q86 OCA], [https://pdbe.org/1q86 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q86 RCSB], [https://www.ebi.ac.uk/pdbsum/1q86 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q86 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326]
 +
== 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/q8/1q86_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=1q86 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.
-
===Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit.===
+
Structural insights into peptide bond formation.,Hansen JL, Schmeing TM, Moore PB, Steitz TA Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11670-5. Epub 2002 Aug 16. PMID:12185246<ref>PMID:12185246</ref>
-
{{ABSTRACT_PUBMED_12185246}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 1q86" style="background-color:#fffaf0;"></div>
-
[[1q86]] is a 32 chain structure 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=1Q86 OCA].
+
==See Also==
==See Also==
-
*[[Ribosomal protein L10|Ribosomal protein L10]]
+
*[[Ribosome 3D structures|Ribosome 3D structures]]
-
*[[Ribosomal protein L13|Ribosomal protein L13]]
+
== References ==
-
*[[Ribosomal protein L14|Ribosomal protein L14]]
+
<references/>
-
*[[Ribosomal protein L15|Ribosomal protein L15]]
+
__TOC__
-
*[[Ribosomal protein L2|Ribosomal protein L2]]
+
</StructureSection>
-
*[[Ribosomal protein L3|Ribosomal protein L3]]
+
-
*[[Ribosomal protein L5|Ribosomal protein L5]]
+
-
*[[Ribosomal protein L6|Ribosomal protein L6]]
+
-
*[[Ribosomal protein L7|Ribosomal protein L7]]
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:012185246</ref><references group="xtra"/>
+
[[Category: Haloarcula marismortui]]
[[Category: Haloarcula marismortui]]
-
[[Category: Hansen, J L.]]
+
[[Category: Large Structures]]
-
[[Category: Moore, P B.]]
+
[[Category: Hansen JL]]
-
[[Category: Schmeing, M T.]]
+
[[Category: Moore PB]]
-
[[Category: Steitz, T A.]]
+
[[Category: Schmeing TM]]
-
[[Category: A-site]]
+
[[Category: Steitz TA]]
-
[[Category: P-site]]
+
-
[[Category: Protein-protein complex]]
+
-
[[Category: Protein-rna complex]]
+
-
[[Category: Ribosome]]
+
-
[[Category: Ribosome 50]]
+
-
[[Category: Rna-rna complex]]
+

Current revision

Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit.

PDB ID 1q86

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/1q86"
Personal tools