1dv4: Difference between revisions

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[1dv4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] and [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=1c59 1c59]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=WO2:OCTADECATUNGSTENYL+DIPHOSPHATE'>WO2</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene>, <scene name='pdbligand=WO2:OCTADECATUNGSTENYL+DIPHOSPHATE'>WO2</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=1dv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv4 OCA], [https://pdbe.org/1dv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv4 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv4 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[https://www.uniprot.org/uniprot/RS5_GEOSE RS5_GEOSE]] With S4 and S12 plays an important role in translational accuracy (By similarity).  Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).
+[https://www.uniprot.org/uniprot/RS5_GEOSE RS5_GEOSE] With S4 and S12 plays an important role in translational accuracy (By similarity).  Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=1dv4 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The electron density map of the small ribosomal subunit from Thermus thermophilus, constructed at 4.5 A resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal RNA and proteins. Unbiased assignments, carried out by quantitative covalent binding of heavy atom compounds at predetermined sites, led to the localization of the surface of the ribosomal protein S13 at a position compatible with previous assignments, whereas the surface of S11 was localized at a distance of about twice its diameter from the site suggested for its center by neutron scattering. Proteins S5 and S7, whose structures have been determined crystallographically, were visually placed in the map with no alterations in their conformations. Regions suitable to host the fold of protein S15 were detected in several positions, all at a significant distance from the location of this protein in the neutron scattering map. Targeting the 16S RNA region, where mRNA docks to allow the formation of the initiation complex by a mercurated mRNA analog, led to the characterization of its vicinity.
-The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site.,Tocilj A, Schlunzen F, Janell D, Gluhmann M, Hansen HA, Harms J, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14252-7. PMID:10588692<ref>PMID:10588692</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1dv4" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Ribosomal protein S5|Ribosomal protein S5]]
 *[[Ribosomal protein S7|Ribosomal protein S7]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
@@ Line 40: / Line 29: @@
 [[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Agmon, I]]
+[[Category: Agmon I]]
-[[Category: Bartels, H]]
+[[Category: Bartels H]]
-[[Category: Bashan, A]]
+[[Category: Bashan A]]
-[[Category: Franceschi, F]]
+[[Category: Franceschi F]]
-[[Category: Gluhmann, M]]
+[[Category: Gluhmann M]]
-[[Category: Hansen, H]]
+[[Category: Hansen H]]
-[[Category: Harms, J]]
+[[Category: Harms J]]
-[[Category: Janell, D]]
+[[Category: Janell D]]
-[[Category: Schlunzen, F]]
+[[Category: Schlunzen F]]
-[[Category: Tocilj, A]]
+[[Category: Tocilj A]]
-[[Category: Yonath, A]]
+[[Category: Yonath A]]
-[[Category: 16s rna]]
-[[Category: Ribosome]]