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.

2uxd

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

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

2uxd is a 23 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	1fjg, 1gix, 1i94, 1i95, 1i96, 1i97, 1ibk, 1ibl, 1ibm, 1j5e, 1jgo, 1jgp, 1jgq, 1l1u, 1n32, 1n33, 1n34, 1n36, 1pns, 1pnx, 1xmo, 1xmq, 1xnq, 1xnr, 1yl4, 2b64, 2b9m, 2b9o, 2f4v, 2j00, 2j02, 2uu9, 2uua, 2uub, 2uuc, 2uxb, 2uxc
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RS16_THET8] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [RS6_THET8] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [RS9_THET8] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [RS8_THET8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B]

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

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.

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^[1]

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

References

↑ Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V. Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit. RNA. 2007 Jun;13(6):817-23. Epub 2007 Apr 6. PMID:17416634 doi:http://dx.doi.org/10.1261/rna.367307

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/2uxd"

@@ Line 1: / Line 1: @@
 ==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=''>
+<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 23 chain structure with sequence 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2UXD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2uxd]] is a 23 chain structure with sequence from [https://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]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UXD FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><br>
+</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><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fjg|1fjg]], [[1gix|1gix]], [[1i94|1i94]], [[1i95|1i95]], [[1i96|1i96]], [[1i97|1i97]], [[1ibk|1ibk]], [[1ibl|1ibl]], [[1ibm|1ibm]], [[1j5e|1j5e]], [[1jgo|1jgo]], [[1jgp|1jgp]], [[1jgq|1jgq]], [[1l1u|1l1u]], [[1n32|1n32]], [[1n33|1n33]], [[1n34|1n34]], [[1n36|1n36]], [[1pns|1pns]], [[1pnx|1pnx]], [[1xmo|1xmo]], [[1xmq|1xmq]], [[1xnq|1xnq]], [[1xnr|1xnr]], [[1yl4|1yl4]], [[2b64|2b64]], [[2b9m|2b9m]], [[2b9o|2b9o]], [[2f4v|2f4v]], [[2j00|2j00]], [[2j02|2j02]], [[2uu9|2uu9]], [[2uua|2uua]], [[2uub|2uub]], [[2uuc|2uuc]], [[2uxb|2uxb]], [[2uxc|2uxc]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fjg|1fjg]], [[1gix|1gix]], [[1i94|1i94]], [[1i95|1i95]], [[1i96|1i96]], [[1i97|1i97]], [[1ibk|1ibk]], [[1ibl|1ibl]], [[1ibm|1ibm]], [[1j5e|1j5e]], [[1jgo|1jgo]], [[1jgp|1jgp]], [[1jgq|1jgq]], [[1l1u|1l1u]], [[1n32|1n32]], [[1n33|1n33]], [[1n34|1n34]], [[1n36|1n36]], [[1pns|1pns]], [[1pnx|1pnx]], [[1xmo|1xmo]], [[1xmq|1xmq]], [[1xnq|1xnq]], [[1xnr|1xnr]], [[1yl4|1yl4]], [[2b64|2b64]], [[2b9m|2b9m]], [[2b9o|2b9o]], [[2f4v|2f4v]], [[2j00|2j00]], [[2j02|2j02]], [[2uu9|2uu9]], [[2uua|2uua]], [[2uub|2uub]], [[2uuc|2uuc]], [[2uxb|2uxb]], [[2uxc|2uxc]]</div></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2uxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uxd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2uxd RCSB], [http://www.ebi.ac.uk/pdbsum/2uxd 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=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>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[https://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[https://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[https://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_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>
+    <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/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=2uxd ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2uxd" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ribosomal protein THX|Ribosomal protein THX]]
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
 *[[Ribosome 3D structures|Ribosome 3D structures]]
 == References ==
@@ Line 33: / Line 37: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Dunham, C M.]]
+[[Category: Dunham, C M]]
-[[Category: Joseph, S.]]
+[[Category: Joseph, S]]
-[[Category: Kelley, A C.]]
+[[Category: Kelley, A C]]
-[[Category: Phelps, S S.]]
+[[Category: Phelps, S S]]
-[[Category: Ramakrishnan, V.]]
+[[Category: Ramakrishnan, V]]
-[[Category: Selmer, M.]]
+[[Category: Selmer, M]]
-[[Category: Suzuki, T.]]
+[[Category: Suzuki, T]]
 [[Category: 30s ribosomal subunit]]
 [[Category: A site]]

2uxd

From Proteopedia

Current revision

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

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox