View source for 1nkw


==Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans==
<StructureSection load='1nkw' size='340' side='right'caption='[[1nkw]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1nkw]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lnr 1lnr], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kpj 1kpj] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc9 1kc9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKW FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1njm|1njm]], [[1njn|1njn]], [[1njo|1njo]], [[1njp|1njp]], [[1k01|1k01]], [[1jzx|1jzx]], [[1jzy|1jzy]], [[1jzz|1jzz]], [[1k00|1k00]]</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkw OCA], [http://pdbe.org/1nkw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nkw RCSB], [http://www.ebi.ac.uk/pdbsum/1nkw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkw ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/RL14_DEIRA RL14_DEIRA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL24_DEIRA RL24_DEIRA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_B]  One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (TF) when it is bound to the ribosome; this contact may expose a hydrophobic crevice in TF (PubMed:16271892).[HAMAP-Rule:MF_01326_B] [[http://www.uniprot.org/uniprot/RL6_DEIRA RL6_DEIRA]] It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center (By similarity). This protein binds to the 23S rRNA, and is important in its secondary structure.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL31_DEIRA RL31_DEIRA]] Binds the 23S rRNA and interacts with the tRNA in the E site.[HAMAP-Rule:MF_00501] [[http://www.uniprot.org/uniprot/RL20_DEIRA RL20_DEIRA]] Binds directly to 23S rRNA, probably serving to organize its structure.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL25_DEIRA RL25_DEIRA]] This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit. This protein has three domains. The N-terminal one is bound on the solvent face, the middle domain fills the space between the 5S rRNA and the L11 arm contacting the 23S rRNA while the C-terminal domain is on the edge of the intersubunit interface and contacts the A site. The protein conformation changes upon binding of a tRNA mimic to the A site, although the mimic does not interact directly with CTC itself, consistent with CTCs presumed role in moderating A site binding.[HAMAP-Rule:MF_01334] [[http://www.uniprot.org/uniprot/RL21_DEIRA RL21_DEIRA]] Binds directly to 23S rRNA, probably serving to organize its structure.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL35_DEIRA RL35_DEIRA]] Binds the 23S rRNA.[HAMAP-Rule:MF_00514] [[http://www.uniprot.org/uniprot/RL27_DEIRA RL27_DEIRA]] Binds the 5S and 23S rRNAs and also the tRNA in the P site.[HAMAP-Rule:MF_00539] [[http://www.uniprot.org/uniprot/RL16_DEIRA RL16_DEIRA]] Binds the 5S and 23S rRNAs and is also seen to make contacts with the A and P site tRNAs. Interacts with A site tRNA mimics, and is probably one of the key factors, along with a helix of the 23S rRNA, in positioning tRNA stems in the peptidyl-transferase center.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL19_DEIRA RL19_DEIRA]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site (By similarity). Binds the 23S rRNA.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL34_DEIRA RL34_DEIRA]] Binds the 23S rRNA.[HAMAP-Rule:MF_00391] [[http://www.uniprot.org/uniprot/RL5_DEIRA RL5_DEIRA]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement (By similarity). Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RL32_DEIRA RL32_DEIRA]] Forms a cluster with L17 and L22, and with L22, a pair of "tweezers" that hold together all the domains of the 23S rRNA. Interacts with the antibiotic troleandomycin which blocks the peptide exit tunnel.[HAMAP-Rule:MF_00340] [[http://www.uniprot.org/uniprot/RL30_DEIRA RL30_DEIRA]] Binds the 5S and 23S rRNAs.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL33_DEIRA RL33_DEIRA]] Binds the 23S rRNA and the E site tRNA.[HAMAP-Rule:MF_00294] [[http://www.uniprot.org/uniprot/RL2_DEIRA RL2_DEIRA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL11_DEIRA RL11_DEIRA]] This protein binds directly to 23S ribosomal RNA and also contacts the CTC protein (RL25).[HAMAP-Rule:MF_00736_B] [[http://www.uniprot.org/uniprot/RL15_DEIRA RL15_DEIRA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RL17_DEIRA RL17_DEIRA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01368] [[http://www.uniprot.org/uniprot/RL18_DEIRA RL18_DEIRA]] This is one of the proteins that binds and mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.[HAMAP-Rule:MF_01337_B] [[http://www.uniprot.org/uniprot/RL23_DEIRA RL23_DEIRA]] One of the early assembly protein (By similarity) it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Forms the main docking site for trigger factor binding to the ribosome (PubMed:16091460 and PubMed:16271892).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL9_DEIRA RL9_DEIRA]] Binds to the 23S rRNA and protein L31.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL3_DEIRA RL3_DEIRA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL29_DEIRA RL29_DEIRA]] Binds the 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL13_DEIRA RL13_DEIRA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to the 23S rRNA.[HAMAP-Rule:MF_01366_B] [[http://www.uniprot.org/uniprot/RL22_DEIRA RL22_DEIRA]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331_B]  The globular domain of the protein is located by the polypeptide exit tunnel on the outside of the subunit while an extended beta-hairpin forms part of the wall of the tunnel. Forms a pair of "tweezers" with L32 that hold together two different domains of the 23S rRNA. Interacts with the tunnel-blocking modified macrolide azithromycin. Upon binding of the macrolide troleadomycin to the ribosome, the tip of the beta-hairpin is displaced, which severely restricts the tunnel. This and experiments in E.coli have led to the suggestion that it is part of the gating mechanism involved in translation arrest in the absence of the protein export system.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL36_DEIRA RL36_DEIRA]] Binds the 23S rRNA.[HAMAP-Rule:MF_00251] [[http://www.uniprot.org/uniprot/RL4_DEIRA RL4_DEIRA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_B]  Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_B]  This protein is located close to the polypeptide exit tunnel, and interacts with the modified macrolide azithromycin, which blocks the tunnel.[HAMAP-Rule:MF_01328_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/nk/1nkw_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=1nkw ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We describe the high resolution structure of the large ribosomal subunit from Deinococcus radiodurans (D50S), a gram-positive mesophile suitable for binding of antibiotics and functionally relevant ligands. The over-all structure of D50S is similar to that from the archae bacterium Haloarcula marismortui (H50S); however, a detailed comparison revealed significant differences, for example, in the orientation of nucleotides in peptidyl transferase center and in the structures of many ribosomal proteins. Analysis of ribosomal features involved in dynamic aspects of protein biosynthesis that are partially or fully disordered in H50S revealed the conformations of intersubunit bridges in unbound subunits, suggesting how they may change upon subunit association and how movements of the L1-stalk may facilitate the exit of tRNA.

High resolution structure of the large ribosomal subunit from a mesophilic eubacterium.,Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A Cell. 2001 Nov 30;107(5):679-88. PMID:11733066<ref>PMID:11733066</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1nkw" style="background-color:#fffaf0;"></div>

==See Also==
*[[Kink-turn motif|Kink-turn motif]]
*[[Large Ribosomal Subunit of Haloarcula|Large Ribosomal Subunit of Haloarcula]]
*[[Ribosome|Ribosome]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit|User:Wayne Decatur/Haloarcula Large Ribosomal Subunit]]
*[[User:Wayne Decatur/kink-turn motif|User:Wayne Decatur/kink-turn motif]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Deinococcus radiodurans]]
[[Category: Large Structures]]
[[Category: Agmon, I]]
[[Category: Bartels, H]]
[[Category: Bashan, A]]
[[Category: Franceschi, F]]
[[Category: Gat, S]]
[[Category: Harms, J M]]
[[Category: Schluenzen, F]]
[[Category: Yonath, A]]
[[Category: Zarivach, R]]
[[Category: Deinococcus radioduran]]
[[Category: Large subunit]]
[[Category: Peptide bond formation]]
[[Category: Peptidyl-transferase]]
[[Category: Ribosome]]
[[Category: X-ray structure]]