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.


1dmg

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1dmg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dmg, resolution 1.7&Aring;" /> '''CRYSTAL STRUCTURE OF ...)
Current revision (06:56, 7 February 2024) (edit) (undo)
 
(18 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dmg.gif|left|200px]]<br /><applet load="1dmg" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1dmg, resolution 1.7&Aring;" />
 
-
'''CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L4'''<br />
 
-
==Overview==
+
==CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L4==
-
Ribosomal protein L4 resides near the peptidyl transferase center of the, bacterial ribosome and may, together with rRNA and proteins L2 and L3, actively participate in the catalysis of peptide bond formation., Escherichia coli L4 is also an autogenous feedback regulator of, transcription and translation of the 11 gene S10 operon. The crystal, structure of L4 from Thermotoga maritima at 1.7 A resolution shows the, protein with an alternating alpha/beta fold and a large disordered loop, region. Two separate binding sites for RNA are discernible. The N-terminal, site, responsible for binding to rRNA, consists of the disordered loop, with flanking alpha-helices. The C-terminal site, a prime candidate for, the interaction with the leader sequence of the S10 mRNA, involves two, non-consecutive alpha-helices. The structure also suggests a C-terminal, protein-binding interface, through which L4 could be interacting with, protein components of the transcriptional and/or translational, machineries.
+
<StructureSection load='1dmg' size='340' side='right'caption='[[1dmg]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1dmg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DMG FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene></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=1dmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmg OCA], [https://pdbe.org/1dmg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dmg RCSB], [https://www.ebi.ac.uk/pdbsum/1dmg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dmg ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RL4_THEMA RL4_THEMA] 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. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01328_B] This protein only weakly controls expression of the E.coli S10 operon. It is incorporated into E.coli ribosomes, however it is not as firmly associated as the endogenous protein.[HAMAP-Rule:MF_01328_B] Forms part of the polypeptide exit tunnel (By similarity).[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/dm/1dmg_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=1dmg ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1DMG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with CIT as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DMG OCA].
+
*[[Ribosomal protein L4|Ribosomal protein L4]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon., Worbs M, Huber R, Wahl MC, EMBO J. 2000 Mar 1;19(5):807-18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10698923 10698923]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
-
[[Category: Huber, R.]]
+
[[Category: Huber R]]
-
[[Category: Wahl, M.C.]]
+
[[Category: Wahl MC]]
-
[[Category: Worbs, M.]]
+
[[Category: Worbs M]]
-
[[Category: CIT]]
+
-
[[Category: alpha-beta]]
+
-
[[Category: l4]]
+
-
[[Category: ribosomal protein]]
+
-
[[Category: ribosome]]
+
-
[[Category: rna]]
+
-
[[Category: s10 operon]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:24:36 2007''
+

Current revision

CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L4

PDB ID 1dmg

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/1dmg"
Personal tools