This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1i6u

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:44, 3 April 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1i6u.gif|left|200px]]
 
-
<!--
+
==RNA-PROTEIN INTERACTIONS: THE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN S8/RRNA COMPLEX FROM METHANOCOCCUS JANNASCHII==
-
The line below this paragraph, containing "STRUCTURE_1i6u", creates the "Structure Box" on the page.
+
<StructureSection load='1i6u' size='340' side='right'caption='[[1i6u]], [[Resolution|resolution]] 2.60&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'>[[1i6u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I6U 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]] 2.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_1i6u| PDB=1i6u | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1i6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i6u OCA], [https://pdbe.org/1i6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i6u RCSB], [https://www.ebi.ac.uk/pdbsum/1i6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i6u ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RS8_METJA RS8_METJA] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity).
 +
== 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/i6/1i6u_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=1i6u ConSurf].
 +
<div style="clear:both"></div>
-
'''RNA-PROTEIN INTERACTIONS: THE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN S8/RRNA COMPLEX FROM METHANOCOCCUS JANNASCHII'''
+
==See Also==
-
 
+
*[[Ribosomal protein S8|Ribosomal protein S8]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The crystal structure of ribosomal protein S8 bound to its target 16 S rRNA from a hyperthermophilic archaeon Methanococcus jannaschii has been determined at 2.6 A resolution. The protein interacts with the minor groove of helix H21 at two sites located one helical turn apart, with S8 forming a bridge over the RNA major groove. The specificity of binding is essentially provided by the C-terminal domain of S8 and the highly conserved nucleotide core, characterized by two dinucleotide platforms, facing each other. The first platform (A595-A596), which is the less phylogenetically and structurally constrained, does not directly contact the protein but has an important shaping role in inducing cross-strand stacking interactions. The second platform (U641-A642) is specifically recognized by the protein. The universally conserved A642 plays a pivotal role by ensuring the cohesion of the complex organization of the core through an array of hydrogen bonds, including the G597-C643-U641 base triple. In addition, A642 provides the unique base-specific interaction with the conserved Ser105, while the Thr106 - Thr107 peptide link is stacked on its purine ring. Noteworthy, the specific recognition of this tripeptide (Thr-Ser-Thr/Ser) is parallel to the recognition of an RNA tetraloop by a dinucleotide platform in the P4-P6 ribozyme domain of group I intron. This suggests a general dual role of dinucleotide platforms in recognition of RNA or peptide motifs. One prominent feature is that conserved side-chain amino acids, as well as conserved bases, are essentially involved in maintaining tertiary folds. The specificity of binding is mainly driven by shape complementarity, which is increased by the hydrophobic part of side-chains. The remarkable similarity of this complex with its homologue in the T. thermophilus 30 S subunit indicates a conserved interaction mode between Archaea and Bacteria.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1I6U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I6U OCA].
+
-
 
+
-
==Reference==
+
-
Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii., Tishchenko S, Nikulin A, Fomenkova N, Nevskaya N, Nikonov O, Dumas P, Moine H, Ehresmann B, Ehresmann C, Piendl W, Lamzin V, Garber M, Nikonov S, J Mol Biol. 2001 Aug 10;311(2):311-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11478863 11478863]
+
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
-
[[Category: Single protein]]
+
[[Category: Dumas P]]
-
[[Category: Dumas, P.]]
+
[[Category: Ehresmann B]]
-
[[Category: Ehresmann, B.]]
+
[[Category: Ehresmann C]]
-
[[Category: Ehresmann, C.]]
+
[[Category: Fomenkova N]]
-
[[Category: Fomenkova, N.]]
+
[[Category: Garber M]]
-
[[Category: Garber, M.]]
+
[[Category: Lamzin V]]
-
[[Category: Lamzin, V.]]
+
[[Category: Moine H]]
-
[[Category: Moine, H.]]
+
[[Category: Nevskaya N]]
-
[[Category: Nevskaya, N.]]
+
[[Category: Nikonov O]]
-
[[Category: Nikonov, O.]]
+
[[Category: Nikonov S]]
-
[[Category: Nikonov, S.]]
+
[[Category: Nikulin A]]
-
[[Category: Nikulin, A.]]
+
[[Category: Piendl W]]
-
[[Category: Piendl, W.]]
+
[[Category: Tishchenko S]]
-
[[Category: Tishchenko, S.]]
+
-
[[Category: Protein-rna interaction]]
+
-
[[Category: Ribosomal protein s8]]
+
-
[[Category: Ribosome]]
+
-
[[Category: Rna]]
+
-
[[Category: X-ray crystallography]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 19:38:31 2008''
+

Current revision

RNA-PROTEIN INTERACTIONS: THE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN S8/RRNA COMPLEX FROM METHANOCOCCUS JANNASCHII

PDB ID 1i6u

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1i6u"
Personal tools