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2h8w

From Proteopedia

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Current revision

Solution structure of ribosomal protein L11

Structural highlights

2h8w is a 1 chain structure with sequence from Thermus thermophilus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL11_THETH This protein binds directly to 23S ribosomal RNA (By similarity).

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

The L11 binding site is one of the most important functional sites in the ribosome. The N-terminal domain of L11 has been implicated as a "reversible switch" in facilitating the coordinated movements associated with EF-G-driven GTP hydrolysis. The reversible switch mechanism has been hypothesized to require conformational flexibility involving re-orientation and re-positioning of the two L11 domains, and warrants a close examination of the structure and dynamics of L11. Here we report the solution structure of free L11, and relaxation studies of free L11, L11 complexed to its 58 nt RNA recognition site, and L11 in a ternary complex with the RNA and thiostrepton antibiotic. The binding site of thiostrepton on L11 was also defined by analysis of structural and dynamics data and chemical shift mapping. The conclusions of this work are as follows: first, the binding of L11 to RNA leads to sizable conformation changes in the regions flanking the linker and in the hinge area that links a beta-sheet and a 3(10)-helix-turn-helix element in the N terminus. Concurrently, the change in the relative orientation may lead to re-positioning of the N terminus, as implied by a decrease of radius of gyration from 18.5 A to 16.2 A. Second, the regions, which undergo large conformation changes, exhibit motions on milliseconds-microseconds or nanoseconds-picoseconds time scales. Third, binding of thiostrepton results in more rigid conformations near the linker (Thr71) and near its putative binding site (Leu12). Lastly, conformational changes in the putative thiostrepton binding site are implicated by the re-emergence of cross-correlation peaks in the spectrum of the ternary complex, which were missing in that of the binary complex. Our combined analysis of both the chemical shift perturbation and dynamics data clearly indicates that thiostrepton binds to a pocket involving residues in the 3(10)-helix in L11.

The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.,Lee D, Walsh JD, Yu P, Markus MA, Choli-Papadopoulou T, Schwieters CD, Krueger S, Draper DE, Wang YX J Mol Biol. 2007 Apr 6;367(4):1007-22. Epub 2007 Jan 10. PMID:17292917^[1]

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

References

↑ Lee D, Walsh JD, Yu P, Markus MA, Choli-Papadopoulou T, Schwieters CD, Krueger S, Draper DE, Wang YX. The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes. J Mol Biol. 2007 Apr 6;367(4):1007-22. Epub 2007 Jan 10. PMID:17292917 doi:10.1016/j.jmb.2007.01.013

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/2h8w"

@@ Line 1: / Line 1: @@
 ==Solution structure of ribosomal protein L11==
-<StructureSection load='2h8w' size='340' side='right' caption='[[2h8w]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2h8w' size='340' side='right'caption='[[2h8w]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2h8w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H8W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H8W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2h8w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H8W FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rplK, rpl11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2h8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h8w OCA], [http://pdbe.org/2h8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2h8w RCSB], [http://www.ebi.ac.uk/pdbsum/2h8w PDBsum]</span></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=2h8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h8w OCA], [https://pdbe.org/2h8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h8w RCSB], [https://www.ebi.ac.uk/pdbsum/2h8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h8w ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RL11_THETH RL11_THETH]] This protein binds directly to 23S ribosomal RNA (By similarity).
+[https://www.uniprot.org/uniprot/RL11_THETH RL11_THETH] This protein binds directly to 23S ribosomal RNA (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/h8/2h8w_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h8/2h8w_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 30: @@
 ==See Also==
-*[[Ribosomal protein L11|Ribosomal protein L11]]
+*[[Ribosomal protein L11 3D structures|Ribosomal protein L11 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
+[[Category: Large Structures]]
-[[Category: Choli-Papadopoulou, T]]
+[[Category: Thermus thermophilus]]
-[[Category: Draper, D]]
+[[Category: Choli-Papadopoulou T]]
-[[Category: Krueger, S]]
+[[Category: Draper D]]
-[[Category: Lee, D]]
+[[Category: Krueger S]]
-[[Category: Walsh, J D]]
+[[Category: Lee D]]
-[[Category: Wang, Y X]]
+[[Category: Walsh JD]]
-[[Category: Yu, P]]
+[[Category: Wang Y-X]]
-[[Category: Antibiotic]]
+[[Category: Yu P]]
-[[Category: L11]]
-[[Category: Ribosome]]
-[[Category: Rna binding protein]]

2h8w

From Proteopedia

Current revision

Solution structure of ribosomal protein L11

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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