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.


1dk1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:51, 20 March 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dk1.gif|left|200px]]
 
-
<!--
+
==DETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL STRUCTURE OF THE S15-RRNA COMPLEX==
-
The line below this paragraph, containing "STRUCTURE_1dk1", creates the "Structure Box" on the page.
+
<StructureSection load='1dk1' size='340' side='right'caption='[[1dk1]], [[Resolution|resolution]] 2.80&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'>[[1dk1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DK1 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]] 2.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-
{{STRUCTURE_1dk1| PDB=1dk1 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dk1 OCA], [https://pdbe.org/1dk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dk1 RCSB], [https://www.ebi.ac.uk/pdbsum/1dk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dk1 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RS15_THETH RS15_THETH] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (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/dk/1dk1_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=1dk1 ConSurf].
 +
<div style="clear:both"></div>
-
'''DETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL STRUCTURE OF THE S15-RRNA COMPLEX'''
+
==See Also==
-
 
+
*[[Ribosomal protein S15|Ribosomal protein S15]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
In bacterial ribosomes, the small (30S) ribosomal subunit is composed of 16S rRNA and 21 distinct proteins. Ribosomal protein S15 is of particular interest because it binds primarily to 16S rRNA and is required for assembly of the small subunit and for intersubunit association, thus representing a key element in the assembly of a whole ribosome. Here we report the 2.8 inverted question mark resolution crystal structure of the highly conserved S15-rRNA complex. Protein S15 interacts in the minor groove with a G-U/G-C motif and a three-way junction. The latter is constrained by a conserved base triple and stacking interactions, and locked into place by magnesium ions and protein side chains, mainly through interactions with the unique three-dimensional geometry of the backbone. The present structure gives insights into the dual role of S15 in ribosome assembly and translational regulation.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1DK1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DK1 OCA].
+
-
 
+
-
==Reference==
+
-
Crystal structure of the S15-rRNA complex., Nikulin A, Serganov A, Ennifar E, Tishchenko S, Nevskaya N, Shepard W, Portier C, Garber M, Ehresmann B, Ehresmann C, Nikonov S, Dumas P, Nat Struct Biol. 2000 Apr;7(4):273-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10742169 10742169]
+
-
[[Category: Single protein]]
+
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
-
[[Category: Ennifar, E.]]
+
[[Category: Ennifar E]]
-
[[Category: Nevskaya, N.]]
+
[[Category: Nevskaya N]]
-
[[Category: Nikulin, A.]]
+
[[Category: Nikulin A]]
-
[[Category: Serganov, A.]]
+
[[Category: Serganov A]]
-
[[Category: Tischenko, S.]]
+
[[Category: Tischenko S]]
-
[[Category: Protein]]
+
-
[[Category: Ribosome]]
+
-
[[Category: Rna]]
+
-
[[Category: S15]]
+
-
[[Category: X-ray]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:56:15 2008''
+

Current revision

DETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL STRUCTURE OF THE S15-RRNA COMPLEX

PDB ID 1dk1

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/1dk1"
Personal tools