1dv4: Difference between revisions

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{{Seed}}
[[Image:1dv4.png|left|200px]]


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==PARTIAL STRUCTURE OF 16S RNA OF THE SMALL RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS==
The line below this paragraph, containing "STRUCTURE_1dv4", creates the "Structure Box" on the page.
<StructureSection load='1dv4' size='340' side='right'caption='[[1dv4]], [[Resolution|resolution]] 4.50&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'>[[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]. 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>
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]] 4.5&#8491;</td></tr>
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<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>
{{STRUCTURE_1dv4|  PDB=1dv4  |  SCENE=  }}
<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]
== 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/dv/1dv4_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=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.


===PARTIAL STRUCTURE OF 16S RNA OF THE SMALL RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS===
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>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_10588692}}, adds the Publication Abstract to the page
*[[Ribosomal protein S5|Ribosomal protein S5]]
(as it appears on PubMed at http://www.pubmed.gov), where 10588692 is the PubMed ID number.
*[[Ribosomal protein S7|Ribosomal protein S7]]
-->
== References ==
{{ABSTRACT_PUBMED_10588692}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
1DV4 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] and [http://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].
 
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/10588692 10588692]
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[Category: Agmon, I.]]
[[Category: Bartels, H.]]
[[Category: Bashan, A.]]
[[Category: Franceschi, F.]]
[[Category: Gluhmann, M.]]
[[Category: Hansen, H.]]
[[Category: Harms, J.]]
[[Category: Janell, D.]]
[[Category: Schlunzen, F.]]
[[Category: Tocilj, A.]]
[[Category: Yonath, A.]]
[[Category: 16s rna]]
[[Category: 30]]
[[Category: Ribosome]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
 
[[Category: Agmon I]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 23:39:50 2008''
[[Category: Bartels H]]
[[Category: Bashan A]]
[[Category: Franceschi F]]
[[Category: Gluhmann M]]
[[Category: Hansen H]]
[[Category: Harms J]]
[[Category: Janell D]]
[[Category: Schlunzen F]]
[[Category: Tocilj A]]
[[Category: Yonath A]]
Retrieved from "https://proteopedia.org/1dv4"