1j5e: Difference between revisions

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-[[Image:1j5e.gif|left|200px]]
- {{Structure
+==Structure of the Thermus thermophilus 30S Ribosomal Subunit==
-|PDB= 1j5e |SIZE=350|CAPTION= <scene name='initialview01'>1j5e</scene>, resolution 3.05&Aring;
+<StructureSection load='1j5e' size='340' side='right'caption='[[1j5e]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[1j5e]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fjf 1fjf]. 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=1J5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J5E FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.05&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5e OCA], [https://pdbe.org/1j5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j5e RCSB], [https://www.ebi.ac.uk/pdbsum/1j5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j5e ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1qd7|1QD7]], [[1fjg|1FJG]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5e OCA], [http://www.ebi.ac.uk/pdbsum/1j5e PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1j5e RCSB]</span>
+== 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/j5/1j5e_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=1j5e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 A resolution. The final atomic model rationalizes over four decades of biochemical data on the ribosome, and provides a wealth of information about RNA and protein structure, protein-RNA interactions and ribosome assembly. It is also a structural basis for analysis of the functions of the 30S subunit, such as decoding, and for understanding the action of antibiotics. The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography.
-'''Structure of the Thermus thermophilus 30S Ribosomal Subunit'''
+Structure of the 30S ribosomal subunit.,Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V Nature. 2000 Sep 21;407(6802):327-39. PMID:11014182<ref>PMID:11014182</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1j5e" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 A resolution. The final atomic model rationalizes over four decades of biochemical data on the ribosome, and provides a wealth of information about RNA and protein structure, protein-RNA interactions and ribosome assembly. It is also a structural basis for analysis of the functions of the 30S subunit, such as decoding, and for understanding the action of antibiotics. The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography.
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
+*[[Ribosome|Ribosome]]
-==About this Structure==
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-J5E is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes the now removed PDB entry 1FJF. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5E OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-Structure of the 30S ribosomal subunit., Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V, Nature. 2000 Sep 21;407(6802):327-39. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11014182 11014182]
+</StructureSection>
-[[Category: Protein complex]]
+[[Category: Aminoglycoside Antibiotics]]
+[[Category: Large Structures]]
+[[Category: RCSB PDB Molecule of the Month]]
 [[Category: Thermus thermophilus]]
-[[Category: Brodersen, D E.]]
+[[Category: Brodersen DE]]
-[[Category: Carter, A P.]]
+[[Category: Carter AP]]
-[[Category: Hartsch, T.]]
+[[Category: Clemons Jr WM]]
-[[Category: Jr., W M.Clemons.]]
+[[Category: Hartsch T]]
-[[Category: Morgan-Warren, R.]]
+[[Category: Morgan-Warren R]]
-[[Category: Ramakrishnan, V.]]
+[[Category: Ramakrishnan V]]
-[[Category: Vonrhein, C.]]
+[[Category: Vonrhein C]]
-[[Category: Wimberly, B T.]]
+[[Category: Wimberly BT]]
-[[Category: 30s ribosomal subunit]]
-[[Category: ribosome]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:29:08 2008''