1xnq

From Proteopedia

(Difference between revisions)

@@ Line 1: / Line 1: @@
 ==Structure of an Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center==
-<StructureSection load='1xnq' size='340' side='right' caption='[[1xnq]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
+<StructureSection load='1xnq' size='340' side='right'caption='[[1xnq]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xnq]] 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=1XNQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XNQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xnq]] is a 10 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=1XNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XNQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.05&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=I:INOSINIC+ACID'>I</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xmo|1xmo]], [[1xmq|1xmq]], [[1ibl|1ibl]], [[1ibm|1ibm]]</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=1xnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xnq OCA], [https://pdbe.org/1xnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xnq RCSB], [https://www.ebi.ac.uk/pdbsum/1xnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xnq ProSAT]</span></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=1xnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xnq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xnq RCSB], [http://www.ebi.ac.uk/pdbsum/1xnq PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RS19_THETH RS19_THETH]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B]  Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[HAMAP-Rule:MF_01307_B] [[http://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] 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 by binding and bridging several RNA helices of the 16S rRNA.  Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS16_THETH RS16_THETH]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains. [[http://www.uniprot.org/uniprot/RSHX_THETH RSHX_THETH]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS10_THETH RS10_THETH]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS18_THETH RS18_THETH]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS17_THET2 RS17_THET2]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity).
+[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/xn/1xnq_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xn/1xnq_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <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/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=1xnq ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1xnq" style="background-color:#fffaf0;"></div>
 ==See Also==
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
 *[[Ribosome 3D structures|Ribosome 3D structures]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Murphy, F V]]
+[[Category: Murphy FV]]
-[[Category: Ramakrishnan, V]]
+[[Category: Ramakrishnan V]]
-[[Category: Decoding]]
-[[Category: Inosine]]
-[[Category: Ribosome]]
-[[Category: Translation]]

Current revision

Structure of an Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center

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PDB ID 1xnq

Show:Asymmetric Unit Biological Assembly

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Structural highlights

1xnq is a 10 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.05Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

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

Publication Abstract from PubMed

Here we report the crystal structures of I.C and I.A wobble base pairs in the context of the ribosomal decoding center, clearly showing that the I.A base pair is of an I(anti).A(anti) conformation, as predicted by Crick. Additionally, the structures enable the observation of changes in the anticodon to allow purine-purine base pairing, the 'widest' base pair geometry allowed in the wobble position.

Structure of a purine-purine wobble base pair in the decoding center of the ribosome.,Murphy FV 4th, Ramakrishnan V Nat Struct Mol Biol. 2004 Dec;11(12):1251-2. Epub 2004 Nov 21. PMID:15558050^[1]

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

References

↑ Murphy FV 4th, Ramakrishnan V. Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Nat Struct Mol Biol. 2004 Dec;11(12):1251-2. Epub 2004 Nov 21. PMID:15558050 doi:http://dx.doi.org/10.1038/nsmb866

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

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Categories: Large Structures | Thermus thermophilus | Murphy FV | Ramakrishnan V

1xnq

From Proteopedia

Current revision

Structure of an Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center

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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