1ibm: Difference between revisions

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-[[Image:1ibm.png|left|200px]]
-<!--
+==STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE==
-The line below this paragraph, containing "STRUCTURE_1ibm", creates the "Structure Box" on the page.
+<StructureSection load='1ibm' size='340' side='right'caption='[[1ibm]], [[Resolution|resolution]] 3.31&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'>[[1ibm]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The February 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoglycoside Antibiotics''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_2 10.2210/rcsb_pdb/mom_2012_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IBM 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]] 3.31&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1ibm|  PDB=1ibm  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ibm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibm OCA], [https://pdbe.org/1ibm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ibm RCSB], [https://www.ebi.ac.uk/pdbsum/1ibm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ibm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
+== 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/ib/1ibm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1ibm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.
-===STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE===
+Recognition of cognate transfer RNA by the 30S ribosomal subunit.,Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V Science. 2001 May 4;292(5518):897-902. PMID:11340196<ref>PMID:11340196</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_11340196}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ibm" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11340196 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_11340196}}
-==About this Structure==
-[[1ibm]] is a 24 chain structure of [[Ribosomal protein S10]], [[Ribosomal protein S11]], [[Ribosomal protein S12]], [[Ribosomal protein S13]], [[Ribosomal protein S15]], [[Ribosomal protein S17]], [[Ribosomal protein S2]], [[Ribosomal protein S20]], [[Ribosomal protein S3]], [[Ribosomal protein S4]] and [[Ribosome]] with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBM OCA].
 ==See Also==
-*[[Ribosomal protein S10]]
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
-*[[Ribosomal protein S11]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[Ribosomal protein S12]]
+== References ==
-*[[Ribosomal protein S13]]
+<references/>
-*[[Ribosomal protein S15]]
+__TOC__
-*[[Ribosomal protein S17]]
+</StructureSection>
-*[[Ribosomal protein S2]]
+[[Category: Aminoglycoside Antibiotics]]
-*[[Ribosomal protein S20]]
+[[Category: Large Structures]]
-*[[Ribosomal protein S3]]
+[[Category: RCSB PDB Molecule of the Month]]
-*[[Ribosomal protein S4]]
-*[[Ribosome]]
-==Reference==
-<ref group="xtra">PMID:11340196</ref><references group="xtra"/>
 [[Category: Thermus thermophilus]]
-[[Category: Brodersen, D E.]]
+[[Category: Brodersen DE]]
-[[Category: Carter, A P.]]
+[[Category: Carter AP]]
-[[Category: Clemons, W M.]]
+[[Category: Clemons Jr WM]]
-[[Category: Ogle, J M.]]
+[[Category: Ogle JM]]
-[[Category: Ramakrishnan, V.]]
+[[Category: Ramakrishnan V]]
-[[Category: Tarry, M J.]]
+[[Category: Tarry MJ]]
-[[Category: 30s ribosomal subunit]]
-[[Category: A site]]
-[[Category: Anticodon]]
-[[Category: Codon]]
-[[Category: Decoding]]
-[[Category: Messenger rna]]
-[[Category: Mrna]]
-[[Category: Ribosome]]
-[[Category: Stem-loop]]
-[[Category: Transfer trna]]