2d3o

From Proteopedia

(Difference between revisions)

Revision as of 06:35, 30 May 2018

Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans

Structural highlights

2d3o is a 4 chain structure with sequence from "micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960 and Deinococcus radiodurans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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] [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] [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] [TIG_DEIRA] Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase (By similarity). Probably changes conformation upon binding to the ribosome (maybe in particular due to interaction with L24, PubMed:16271892), exposing a hydrophobic crevice that is probably important for its chaperone activity (PubMed:16091460 and PubMed:16271892).[HAMAP-Rule:MF_00303]

Evolutionary Conservation

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

Publication Abstract from PubMed

This study presents the X-ray structure of the N-terminal binding domain of the D. radiodurans trigger factor (TF) in complex with the D. radiodurans large ribosomal subunit. At 3.35 A, a complete description of the interactions with ribosomal proteins L23, L29, and 23S rRNA are disclosed, many of which differ from those found previously for a heterologous bacterial-archaeal TF-ribosome complex. The beta hairpin loop of eubacterial L24, which is shorter in archaeal ribosomes, contacts the TF and severely diminishes the molecular cradle proposed to exist between the TF and ribosome. Bound to the ribosome, TF exposes a hydrophobic crevice large enough to accommodate the nascent polypeptide chain. Superimposition of the full-length TF and the signal-recognition particle (SRP) onto the complex shows that simultaneous cohabitation is possible, in agreement with biochemical data, and suggests a model for the interplay of TF, SRP, and the nascent chain during translation.

The binding mode of the trigger factor on the ribosome: implications for protein folding and SRP interaction.,Schlunzen F, Wilson DN, Tian P, Harms JM, McInnes SJ, Hansen HA, Albrecht R, Buerger J, Wilbanks SM, Fucini P Structure. 2005 Nov;13(11):1685-94. PMID:16271892^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Schlunzen F, Wilson DN, Tian P, Harms JM, McInnes SJ, Hansen HA, Albrecht R, Buerger J, Wilbanks SM, Fucini P. The binding mode of the trigger factor on the ribosome: implications for protein folding and SRP interaction. Structure. 2005 Nov;13(11):1685-94. PMID:16271892 doi:http://dx.doi.org/10.1016/j.str.2005.08.007

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2d3o"

@@ Line 1: / Line 1: @@
 ==Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans==
 <StructureSection load='2d3o' size='340' side='right' caption='[[2d3o]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2d3o]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960] and [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D3O FirstGlance]. <br>
-</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=2d3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3o OCA], [http://pdbe.org/2d3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d3o RCSB], [http://www.ebi.ac.uk/pdbsum/2d3o PDBsum]</span></td></tr>
+</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=2d3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3o OCA], [http://pdbe.org/2d3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d3o RCSB], [http://www.ebi.ac.uk/pdbsum/2d3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3o ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 11: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/2d3o_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/2d3o_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2d3o ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

2d3o

From Proteopedia

Revision as of 06:35, 30 May 2018

Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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