1jgp: Difference between revisions

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-[[Image:1jgp.png|left|200px]]
-<!--
+==The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGP, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY==
-The line below this paragraph, containing "STRUCTURE_1jgp", creates the "Structure Box" on the page.
+<StructureSection load='1jgp' size='340' side='right'caption='[[1jgp]], [[Resolution|resolution]] 7.00&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'>[[1jgp]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JGP 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]] 7&#8491;</td></tr>
--->
+<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=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=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>
-{{STRUCTURE_1jgp|  PDB=1jgp  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jgp OCA], [https://pdbe.org/1jgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jgp RCSB], [https://www.ebi.ac.uk/pdbsum/1jgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jgp 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/jg/1jgp_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=1jgp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Using X-ray crystallography, we have directly observed the path of mRNA in the 70S ribosome in Fourier difference maps at 7 A resolution. About 30 nucleotides of the mRNA are wrapped in a groove that encircles the neck of the 30S subunit. The Shine-Dalgarno helix is bound in a large cleft between the head and the back of the platform. At the interface, only about eight nucleotides (-1 to +7), centered on the junction between the A and P codons, are exposed, and bond almost exclusively to 16S rRNA. The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate -1 translational frame shifting.
-===The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGP, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY===
+The path of messenger RNA through the ribosome.,Yusupova GZ, Yusupov MM, Cate JH, Noller HF Cell. 2001 Jul 27;106(2):233-41. PMID:11511350<ref>PMID:11511350</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_11511350}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1jgp" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11511350 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_11511350}}
-==About this Structure==
-[[1jgp]] is a 25 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 [[Ribosomal protein THX]] 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=1JGP 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]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-*[[Ribosomal protein S13]]
+== References ==
-*[[Ribosomal protein S15]]
+<references/>
-*[[Ribosomal protein S17]]
+__TOC__
-*[[Ribosomal protein S2]]
+</StructureSection>
-*[[Ribosomal protein S20]]
+[[Category: Large Structures]]
-*[[Ribosomal protein S3]]
-*[[Ribosomal protein S4]]
-*[[Ribosomal protein THX]]
-==Reference==
-<ref group="xtra">PMID:11511350</ref><references group="xtra"/>
 [[Category: Thermus thermophilus]]
-[[Category: Cate, J H.D.]]
+[[Category: Cate JHD]]
-[[Category: Noller, H F.]]
+[[Category: Noller HF]]
-[[Category: Yusupov, M M.]]
+[[Category: Yusupov MM]]
-[[Category: Yusupova, G Z.]]
+[[Category: Yusupova GZ]]
-[[Category: Life]]
-[[Category: Protein synthesis]]
-[[Category: Ribosome assembly]]