2uxd: Difference between revisions

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~~[[Image:2uxd.gif|left|200px]]~~

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~~{{STRUCTURE_2uxd| PDB=2uxd | SCENE= }}~~

~~'''CRYSTAL STRUCTURE OF AN EXTENDED TRNA ANTICODON STEM LOOP IN COMPLEX WITH ITS COGNATE MRNA CGGG IN THE CONTEXT OF THE THERMUS THERMOPHILUS 30S SUBUNIT.'''~~

==Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA CGGG in the context of the Thermus thermophilus 30S subunit.==

== Structural highlights ==

<table><tr><td colspan='2'>[[2uxd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UXD 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]] 3.2Å</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=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2uxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uxd OCA], [https://pdbe.org/2uxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uxd RCSB], [https://www.ebi.ac.uk/pdbsum/2uxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uxd ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ux/2uxd_consurf.spt"</scriptWhenChecked>

<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2uxd ConSurf].

== Publication Abstract from PubMed ==

During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor tRNAs that contain an extra base in their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we report crystal structures of two anticodon stem-loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to the 30S ribosomal subunit with their cognate mRNAs. ASL(CCCG) and ASL(ACCC) (5'-3' nomenclature) form unpredicted anticodon-codon interactions where the anticodon base 34 at the wobble position contacts either the fourth codon base or the third and fourth codon bases. In addition, we report the structure of ASL(ACGA) bound to the 30S ribosomal subunit with its cognate mRNA. The tRNA containing this ASL was previously shown to be unable to facilitate +1 frameshifting in competition with normal tRNAs (Hohsaka et al. 2001), and interestingly, it displays a normal anticodon-codon interaction. These structures show that the expanded anticodon loop of +1 frameshift promoting tRNAs are flexible enough to adopt conformations that allow three bases of the anticodon to span four bases of the mRNA. Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center.

~~==Overview==~~

Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit.,Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V RNA. 2007 Jun;13(6):817-23. Epub 2007 Apr 6. PMID:17416634<ref>PMID:17416634</ref>

~~During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor~~ tRNAs ~~that contain~~ an ~~extra base~~ in ~~their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we report crystal structures~~ of ~~two anticodon stem-loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to~~ the 30S ribosomal subunit ~~with their cognate mRNAs~~. ASL(CCCG) and ASL(ACCC) (5'-3' nomenclature) form unpredicted anticodon-codon interactions where the anticodon base 34 at the wobble position contacts either the fourth codon base or the third and fourth codon bases. In addition, ~~we report the structure of ASL(ACGA) bound to the 30S ribosomal subunit with its cognate mRNA~~. ~~The tRNA containing this ASL was previously shown to be unable to facilitate +1 frameshifting in competition with normal tRNAs~~ (~~Hohsaka et al. 2001~~)~~, and interestingly, it displays a normal anticodon~~-codon interaction. These structures show that the expanded anticodon loop of +1 frameshift promoting tRNAs are flexible enough to adopt conformations that allow three bases of the anticodon to span four bases of the mRNA. ~~Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center~~.

~~==About this Structure==~~

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

~~2UXD is~~ a ~~[[Protein complex]] structure~~ of ~~sequences 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=2UXD OCA].~~

</div>

==~~Reference~~==

==See Also==

Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit., Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V, RNA. 2007 Jun;13(6):817-23. Epub 2007 Apr 6. PMID:[~~http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17416634 17416634]~~

*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]

[[Category: ~~Protein complex~~]]

*[[Ribosome 3D structures|Ribosome 3D structures]]

[[Category: Thermus thermophilus]]

== References ==

[[Category: Dunham~~, C M.~~]]

[[Category: Joseph, S.]]

__TOC__

[[Category: Kelley~~, A C.~~]]

</StructureSection>

[[Category: Phelps~~, S S.~~]]

[[Category: Large Structures]]

[[Category: Ramakrishnan, V.]]

[[Category: Thermus thermophilus HB8]]

[[Category: Selmer, M.]]

[[Category: Dunham CM]]

[[Category: Suzuki, T~~.]]~~

[[Category: Joseph S]]

~~[[Category: 30s ribosomal subunit]]~~

[[Category: Kelley AC]]

~~[[Category: A site]]~~

[[Category: Phelps SS]]

~~[[Category: Anticodon]]~~

[[Category: Ramakrishnan V]]

~~[[Category: Codon]]~~

[[Category: Selmer M]]

~~[[Category: Coiled coil]]~~

[[Category: Suzuki T]]

~~[[Category: Decoding]]~~

~~[[Category: Frameshift]]~~

~~[[Category: Frameshift suppressor trna]]~~

~~[[Category: Messenger rna]]~~

~~[[Category: Metal-binding]]~~

~~[[Category: Mrna]]~~

~~[[Category: Paromomycin]]~~

~~[[Category: Ribonucleoprotein]]~~

~~[[Category: Ribosomal protein~~]]

~~[[Category: Ribosome]]~~

~~[[Category: Rna- binding]]~~

~~[[Category: Rna-binding]]~~

~~[[Category: Rrna-binding]]~~

~~[[Category: Stem-loop]]~~

~~[[Category: Transfer rna]]~~

~~[[Category: Trna]]~~

~~[[Category: Trna-binding]]~~

~~[[Category: Zinc]]~~

~~[[Category: Zinc-finger]]~~

~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 17:44:13 2008''~~

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@@ Line 1: / Line 1: @@
-[[Image:2uxd.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2uxd", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2uxd|  PDB=2uxd  |  SCENE=  }}
-'''CRYSTAL STRUCTURE OF AN EXTENDED TRNA ANTICODON STEM LOOP IN COMPLEX WITH ITS COGNATE MRNA CGGG IN THE CONTEXT OF THE THERMUS THERMOPHILUS 30S SUBUNIT.'''
+==Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA CGGG in the context of the Thermus thermophilus 30S subunit.==
+<StructureSection load='2uxd' size='340' side='right'caption='[[2uxd]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2uxd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UXD 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]] 3.2&#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=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2uxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uxd OCA], [https://pdbe.org/2uxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uxd RCSB], [https://www.ebi.ac.uk/pdbsum/2uxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uxd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_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/ux/2uxd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2uxd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor tRNAs that contain an extra base in their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we report crystal structures of two anticodon stem-loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to the 30S ribosomal subunit with their cognate mRNAs. ASL(CCCG) and ASL(ACCC) (5'-3' nomenclature) form unpredicted anticodon-codon interactions where the anticodon base 34 at the wobble position contacts either the fourth codon base or the third and fourth codon bases. In addition, we report the structure of ASL(ACGA) bound to the 30S ribosomal subunit with its cognate mRNA. The tRNA containing this ASL was previously shown to be unable to facilitate +1 frameshifting in competition with normal tRNAs (Hohsaka et al. 2001), and interestingly, it displays a normal anticodon-codon interaction. These structures show that the expanded anticodon loop of +1 frameshift promoting tRNAs are flexible enough to adopt conformations that allow three bases of the anticodon to span four bases of the mRNA. Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center.
-==Overview==
+Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit.,Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V RNA. 2007 Jun;13(6):817-23. Epub 2007 Apr 6. PMID:17416634<ref>PMID:17416634</ref>
-During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor tRNAs that contain an extra base in their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we report crystal structures of two anticodon stem-loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to the 30S ribosomal subunit with their cognate mRNAs. ASL(CCCG) and ASL(ACCC) (5'-3' nomenclature) form unpredicted anticodon-codon interactions where the anticodon base 34 at the wobble position contacts either the fourth codon base or the third and fourth codon bases. In addition, we report the structure of ASL(ACGA) bound to the 30S ribosomal subunit with its cognate mRNA. The tRNA containing this ASL was previously shown to be unable to facilitate +1 frameshifting in competition with normal tRNAs (Hohsaka et al. 2001), and interestingly, it displays a normal anticodon-codon interaction. These structures show that the expanded anticodon loop of +1 frameshift promoting tRNAs are flexible enough to adopt conformations that allow three bases of the anticodon to span four bases of the mRNA. Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-UXD is a [[Protein complex]] structure of sequences 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=2UXD OCA].
+</div>
+<div class="pdbe-citations 2uxd" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit., Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V, RNA. 2007 Jun;13(6):817-23. Epub 2007 Apr 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17416634 17416634]
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
-[[Category: Protein complex]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-[[Category: Thermus thermophilus]]
+== References ==
-[[Category: Dunham, C M.]]
+<references/>
-[[Category: Joseph, S.]]
+__TOC__
-[[Category: Kelley, A C.]]
+</StructureSection>
-[[Category: Phelps, S S.]]
+[[Category: Large Structures]]
-[[Category: Ramakrishnan, V.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Selmer, M.]]
+[[Category: Dunham CM]]
-[[Category: Suzuki, T.]]
+[[Category: Joseph S]]
-[[Category: 30s ribosomal subunit]]
+[[Category: Kelley AC]]
-[[Category: A site]]
+[[Category: Phelps SS]]
-[[Category: Anticodon]]
+[[Category: Ramakrishnan V]]
-[[Category: Codon]]
+[[Category: Selmer M]]
-[[Category: Coiled coil]]
+[[Category: Suzuki T]]
-[[Category: Decoding]]
-[[Category: Frameshift]]
-[[Category: Frameshift suppressor trna]]
-[[Category: Messenger rna]]
-[[Category: Metal-binding]]
-[[Category: Mrna]]
-[[Category: Paromomycin]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome]]
-[[Category: Rna- binding]]
-[[Category: Rna-binding]]
-[[Category: Rrna-binding]]
-[[Category: Stem-loop]]
-[[Category: Transfer rna]]
-[[Category: Trna]]
-[[Category: Trna-binding]]
-[[Category: Zinc]]
-[[Category: Zinc-finger]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 17:44:13 2008''