1lnt: Difference between revisions

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~~[[Image:1lnt.gif|left|200px]]<br /><applet load="1lnt" size="450" color="white" frame="true" align="right" spinBox="true"~~

~~caption="1lnt, resolution 1.7Å" />~~

~~'''Crystal Structure of the Highly Conserved RNA Internal Loop of SRP'''<br />~~

==~~Overview~~==

==Crystal Structure of the Highly Conserved RNA Internal Loop of SRP==

The crystal structure of an RNA dodecamer, r(GCGUCAGGUC(Br)CG)/r(CGGAAGCAG(Br)CGC), containing a fragment from the, signal recognition particle (SRP) RNA (domain IV) of Escherichia coli, has, been determined at 1.7 A resolution with 21 666 independent reflections, and an R(work) and R(free) of 20.1 and 22.5%, respectively. The structure, exhibits a novel crystal packing pattern for RNA oligomer duplexes: one, end of the duplex adopts the stacking interaction, while the other end, adopts the abutting interaction in the minor groove. The symmetric loop of, the SRP, r(CAGG)/r(AGCA), in the center of the dodecamer forms two, different conformations of the A.C mismatch, a sheared G.G and a, symmetrical G.A mismatch. These four mismatches present a unique surface, for the abutting interaction. The involvement of the two A.C mismatches in, the abutting interaction implies that these mismatches are the important, sites for interaction with proteins. The conformation of the symmetric, loop is greatly stabilized by hydrated metal ions, which display, flexibility in adjusting their geometry and coordination in interaction, with nucleic acids. Comparison with other crystal structures of fragments, of 4.5S RNA indicates that the conformation of the symmetric loop is, independent of the asymmetrical loop in domain IV.

== Structural highlights ==

<table><tr><td colspan='2'>[[1lnt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LNT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LNT 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]] 1.7Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CBV:5-BROMOCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CBV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1lnt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lnt OCA], [https://pdbe.org/1lnt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lnt RCSB], [https://www.ebi.ac.uk/pdbsum/1lnt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lnt ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

The crystal structure of an RNA dodecamer, r(GCGUCAGGUC(Br)CG)/r(CGGAAGCAG(Br)CGC), containing a fragment from the signal recognition particle (SRP) RNA (domain IV) of Escherichia coli, has been determined at 1.7 A resolution with 21 666 independent reflections and an R(work) and R(free) of 20.1 and 22.5%, respectively. The structure exhibits a novel crystal packing pattern for RNA oligomer duplexes: one end of the duplex adopts the stacking interaction, while the other end adopts the abutting interaction in the minor groove. The symmetric loop of the SRP, r(CAGG)/r(AGCA), in the center of the dodecamer forms two different conformations of the A.C mismatch, a sheared G.G and a symmetrical G.A mismatch. These four mismatches present a unique surface for the abutting interaction. The involvement of the two A.C mismatches in the abutting interaction implies that these mismatches are the important sites for interaction with proteins. The conformation of the symmetric loop is greatly stabilized by hydrated metal ions, which display flexibility in adjusting their geometry and coordination in interaction with nucleic acids. Comparison with other crystal structures of fragments of 4.5S RNA indicates that the conformation of the symmetric loop is independent of the asymmetrical loop in domain IV.

~~==About this~~ Structure==

Structure of an RNA dodecamer containing a fragment from SRP domain IV of Escherichia coli.,Deng J, Xiong Y, Pan B, Sundaralingam M Acta Crystallogr D Biol Crystallogr. 2003 Jun;59(Pt 6):1004-11. Epub 2003, May 23. PMID:12777762<ref>PMID:12777762</ref>

~~1LNT is~~ a ~~[http://en~~.~~wikipedia~~.~~org/wiki/Protein_complex Protein complex] structure of sequences from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/ ] with MG and CA as [http~~:~~//en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http~~:/~~/ispc.weizmann.ac.il/oca-bin/ocashort?id=1LNT OCA].~~

~~==Reference==~~

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

~~Structure of an RNA dodecamer containing~~ a ~~fragment from SRP domain IV~~ of ~~Escherichia coli~~.~~, Deng J, Xiong Y, Pan B, Sundaralingam M, Acta Crystallogr D Biol Crystallogr~~. ~~2003 Jun;59(Pt 6):1004~~-~~11. Epub 2003, May 23. PMID:[http~~://~~ispc.weizmann.ac.il//pmbin~~/~~getpm?pmid=12777762 12777762]~~

</div>

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

[[Category: Deng, J.]]

== References ==

[[Category: Pan, B.]]

[[Category: Sundaralingam, M.]]

__TOC__

[[Category: Xiong, Y~~.]]~~

</StructureSection>

~~[[Category: CA]]~~

[[Category: Large Structures]]

~~[[Category: MG]]~~

[[Category: Deng J]]

~~[[Category: internal loop]]~~

[[Category: Pan B]]

~~[[Category: mispair]~~]

[[Category: Sundaralingam M]]

~~[[Category: rna~~]]

[[Category: Xiong Y]]

~~[[Category: srp]]~~

~~''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:10:22 2007''~~

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@@ Line 1: / Line 1: @@
-[[Image:1lnt.gif|left|200px]]<br /><applet load="1lnt" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1lnt, resolution 1.7&Aring;" />
-'''Crystal Structure of the Highly Conserved RNA Internal Loop of SRP'''<br />
-==Overview==
+==Crystal Structure of the Highly Conserved RNA Internal Loop of SRP==
-The crystal structure of an RNA dodecamer, r(GCGUCAGGUC(Br)CG)/r(CGGAAGCAG(Br)CGC), containing a fragment from the, signal recognition particle (SRP) RNA (domain IV) of Escherichia coli, has, been determined at 1.7 A resolution with 21 666 independent reflections, and an R(work) and R(free) of 20.1 and 22.5%, respectively. The structure, exhibits a novel crystal packing pattern for RNA oligomer duplexes: one, end of the duplex adopts the stacking interaction, while the other end, adopts the abutting interaction in the minor groove. The symmetric loop of, the SRP, r(CAGG)/r(AGCA), in the center of the dodecamer forms two, different conformations of the A.C mismatch, a sheared G.G and a, symmetrical G.A mismatch. These four mismatches present a unique surface, for the abutting interaction. The involvement of the two A.C mismatches in, the abutting interaction implies that these mismatches are the important, sites for interaction with proteins. The conformation of the symmetric, loop is greatly stabilized by hydrated metal ions, which display, flexibility in adjusting their geometry and coordination in interaction, with nucleic acids. Comparison with other crystal structures of fragments, of 4.5S RNA indicates that the conformation of the symmetric loop is, independent of the asymmetrical loop in domain IV.
+<StructureSection load='1lnt' size='340' side='right'caption='[[1lnt]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1lnt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LNT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LNT 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CBV:5-BROMOCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CBV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1lnt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lnt OCA], [https://pdbe.org/1lnt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lnt RCSB], [https://www.ebi.ac.uk/pdbsum/1lnt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lnt ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of an RNA dodecamer, r(GCGUCAGGUC(Br)CG)/r(CGGAAGCAG(Br)CGC), containing a fragment from the signal recognition particle (SRP) RNA (domain IV) of Escherichia coli, has been determined at 1.7 A resolution with 21 666 independent reflections and an R(work) and R(free) of 20.1 and 22.5%, respectively. The structure exhibits a novel crystal packing pattern for RNA oligomer duplexes: one end of the duplex adopts the stacking interaction, while the other end adopts the abutting interaction in the minor groove. The symmetric loop of the SRP, r(CAGG)/r(AGCA), in the center of the dodecamer forms two different conformations of the A.C mismatch, a sheared G.G and a symmetrical G.A mismatch. These four mismatches present a unique surface for the abutting interaction. The involvement of the two A.C mismatches in the abutting interaction implies that these mismatches are the important sites for interaction with proteins. The conformation of the symmetric loop is greatly stabilized by hydrated metal ions, which display flexibility in adjusting their geometry and coordination in interaction with nucleic acids. Comparison with other crystal structures of fragments of 4.5S RNA indicates that the conformation of the symmetric loop is independent of the asymmetrical loop in domain IV.
-==About this Structure==
+Structure of an RNA dodecamer containing a fragment from SRP domain IV of Escherichia coli.,Deng J, Xiong Y, Pan B, Sundaralingam M Acta Crystallogr D Biol Crystallogr. 2003 Jun;59(Pt 6):1004-11. Epub 2003, May 23. PMID:12777762<ref>PMID:12777762</ref>
-LNT is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG and CA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LNT OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure of an RNA dodecamer containing a fragment from SRP domain IV of Escherichia coli., Deng J, Xiong Y, Pan B, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2003 Jun;59(Pt 6):1004-11. Epub 2003, May 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12777762 12777762]
+</div>
-[[Category: Protein complex]]
+<div class="pdbe-citations 1lnt" style="background-color:#fffaf0;"></div>
-[[Category: Deng, J.]]
+== References ==
-[[Category: Pan, B.]]
+<references/>
-[[Category: Sundaralingam, M.]]
+__TOC__
-[[Category: Xiong, Y.]]
+</StructureSection>
-[[Category: CA]]
+[[Category: Large Structures]]
-[[Category: MG]]
+[[Category: Deng J]]
-[[Category: internal loop]]
+[[Category: Pan B]]
-[[Category: mispair]]
+[[Category: Sundaralingam M]]
-[[Category: rna]]
+[[Category: Xiong Y]]
-[[Category: srp]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:10:22 2007''