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| - | [[Image:1dqf.gif|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF HELIX II OF THE X. LAEVIS SOMATIC 5S RRNA WITH A CYTOSINE BULGE IN TWO CONFORMATIONS== |
| - | |PDB= 1dqf |SIZE=350|CAPTION= <scene name='initialview01'>1dqf</scene>, resolution 2.2Å
| + | <StructureSection load='1dqf' size='340' side='right'caption='[[1dqf]], [[Resolution|resolution]] 2.20Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
| + | <table><tr><td colspan='2'>[[1dqf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQF FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqf OCA], [https://pdbe.org/1dqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dqf RCSB], [https://www.ebi.ac.uk/pdbsum/1dqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dqf ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[idqh|IDQH]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqf OCA], [http://www.ebi.ac.uk/pdbsum/1dqf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dqf RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''CRYSTAL STRUCTURE OF HELIX II OF THE X. LAEVIS SOMATIC 5S RRNA WITH A CYTOSINE BULGE IN TWO CONFORMATIONS'''
| + | [[Category: Sundaralingam M]] |
| - | | + | [[Category: Xiong Y]] |
| - | | + | |
| - | ==Overview==
| + | |
| - | The crystal structure of r(GCCACCCUG).r(CAGGGUCGGC), helix II of the Xenopus laevis 5S rRNA with a cytosine bulge (underlined), has been determined in two forms at 2.2 A (Form I, space group P4(2)2(1)2, a = b = 57.15 A and c = 43.54 A) and 1.7 A (Form II, space group P4(3)2(1)2, a = b = 32.78 A and c = 102.5 A). The helical regions of the nonamers are found in the standard A-RNA conformations and the two forms have an RMS deviation of 0.75 A. However, the cytosine bulge adopts two significantly different conformations with an RMS deviation of 3.9 A. In Form I, the cytosine bulge forms an intermolecular C+*G.C triple in the major groove of a symmetry-related duplex with intermolecular hydrogen bonds between N4C and O6G, and between protonated N3+C and N7G. In contrast, a minor groove C*G.C triple is formed in Form II with intermolecular hydrogen bonds between O2C and N2G, and between N3C and N3G with a water bridge. A partial major groove opening was observed in Form I structure at the bulge site. Two Ca2+ ions were found in Form I helix whereas there were none in Form II. The structural comparison of these two forms indicates that bulged residues can adopt a variety of conformations with little perturbation to the global helix structure. This suggests that bulged residues could function as flexible latches in bridging double helical motifs and facilitate the folding of large RNA molecules.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1DQF is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQF OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge., Xiong Y, Sundaralingam M, RNA. 2000 Sep;6(9):1316-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10999608 10999608]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: Xiong, Y.]] | + | |
| - | [[Category: cytosine bulge]]
| + | |
| - | [[Category: double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:46:44 2008''
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