1c06: Difference between revisions

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New page: left|200px<br /><applet load="1c06" size="450" color="white" frame="true" align="right" spinBox="true" caption="1c06" /> '''SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 D...
 
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[[Image:1c06.gif|left|200px]]<br /><applet load="1c06" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1c06" />
'''SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41, REFINED WITH DIPOLAR COUPLINGS (ENSEMBLE OF 16 STRUCTURES)'''<br />


==Overview==
==SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41, REFINED WITH DIPOLAR COUPLINGS (ENSEMBLE OF 16 STRUCTURES)==
Prokaryotic protein S4 initiates assembly of the small ribosomal subunit, by binding to 16 S rRNA. Residues 43-200 of S4 from Bacillus, stearothermophilus (S4 Delta41) bind to both 16 S rRNA and to a mRNA, pseudoknot. In order to obtain structure-based insights regarding RNA, binding, we previously determined the solution structure of S4 Delta41, using NOE, hydrogen bond, and torsion angle restraints. S4 Delta41 is, elongated, with two distinct subdomains, one all helical, the other, including a beta-sheet. In contrast to the high resolution structures, obtained for each individual subdomain, their relative orientation was not, precisely defined because only 17 intersubdomain NOE restraints were, determined. Compared to the 1.7 A crystal structure, when the, sheet-containing subdomains are superimposed, the helical subdomain is, twisted by almost 45 degrees about the long axis of the molecule in the, solution structure. Because variations in subdomain orientation may, explain how the protein recognizes multiple RNA targets, our current goal, is to determine the orientation of the subdomains in solution with high, precision. To this end, NOE assignments were re-examined. NOESY, experiments on a specifically labeled sample revealed that one of the, intersubdomain restraints had been misassigned. However, the revised set, of NOE restraints produces solution structures that still have imprecisely, defined subdomain orientations and that lie between the original NMR, structure and the crystal structure. In contrast, augmenting the NOE, restraints with N-H dipolar couplings, measured in uniaxial liquid, crystalline phases, clearly establishes the relative orientation of the, subdomains. Data obtained from two independent liquid crystalline milieux, DMPC/DHPC bicelles and the filamentous bacteriophage Pf1, show that the, relative orientation of the subdomains in solution is quite similar to the, subdomain orientation in the crystal structure. The solution structure, refined with dipolar data, is presented and its implications for S4's RNA, binding activity are discussed.
<StructureSection load='1c06' size='340' side='right'caption='[[1c06]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1c06]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C06 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1c06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c06 OCA], [https://pdbe.org/1c06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c06 RCSB], [https://www.ebi.ac.uk/pdbsum/1c06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c06 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RS4_GEOSE RS4_GEOSE] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit (By similarity).[HAMAP-Rule:MF_01306_B]  With S5 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01306_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/c0/1c06_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=1c06 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1C06 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1C06 OCA].
*[[Ribosomal protein S4|Ribosomal protein S4]]
 
__TOC__
==Reference==
</StructureSection>
Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases., Markus MA, Gerstner RB, Draper DE, Torchia DA, J Mol Biol. 1999 Sep 17;292(2):375-87. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10493882 10493882]
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Draper, D.E.]]
[[Category: Draper DE]]
[[Category: Gerstner, R.B.]]
[[Category: Gerstner RB]]
[[Category: Markus, M.A.]]
[[Category: Markus MA]]
[[Category: Torchia, D.A.]]
[[Category: Torchia DA]]
[[Category: possible helix-turn helix motif]]
[[Category: two subdomains]]
[[Category: unique topology]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:03:23 2007''

Latest revision as of 18:37, 13 March 2024

SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41, REFINED WITH DIPOLAR COUPLINGS (ENSEMBLE OF 16 STRUCTURES)SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41, REFINED WITH DIPOLAR COUPLINGS (ENSEMBLE OF 16 STRUCTURES)

Structural highlights

1c06 is a 1 chain structure with sequence from Geobacillus stearothermophilus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS4_GEOSE One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit (By similarity).[HAMAP-Rule:MF_01306_B] With S5 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01306_B]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

Drag the structure with the mouse to rotate

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