|
|
| (11 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | [[Image:1efo.gif|left|200px]] | |
| | | | |
| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG)== |
| - | |PDB= 1efo |SIZE=350|CAPTION= <scene name='initialview01'>1efo</scene>, resolution 2.30Å
| + | <StructureSection load='1efo' size='340' side='right'caption='[[1efo]], [[Resolution|resolution]] 2.30Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>
| + | <table><tr><td colspan='2'>[[1efo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EFO 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]] 2.3Å</td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1efo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1efo OCA], [https://pdbe.org/1efo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1efo RCSB], [https://www.ebi.ac.uk/pdbsum/1efo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1efo ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=
| + | __TOC__ |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1efo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1efo OCA], [http://www.ebi.ac.uk/pdbsum/1efo PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1efo RCSB]</span>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Sudarsanakumar C]] |
| - | '''CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG)'''
| + | [[Category: Sundaralingam M]] |
| - | | + | [[Category: Xiong Y]] |
| - | | + | |
| - | ==Overview==
| + | |
| - | Crystal structure of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag), with an adenine bulge in the polypurine RNA strand was determined at 2.3 A resolution. The structure was solved by the molecular replacement method and refined to a final R-factor of 19.9% (Rfree 22.2%). The hybrid duplex crystallized in the space group I222 with unit cell dimensions, a = 46.66 A, b = 47.61 A and c = 54.05 A, and adopts the A-form conformation. All RNA and DNA sugars are in the C3'-endo conformation, the glycosyl angles in anti conformation and the majority of the C4'-C5' torsion angles in g+ except two trans angles, in conformity with the C3'-endo rigid nucleotide hypothesis. The adenine bulge is looped out and it is also in the anti C3'-endo conformation. The bulge is involved in a base-triple (C.g)*a interaction with the end base-pair (C9.g10) in the minor groove of a symmetry-related molecule. The 2' hydroxyl group of g15 is hydrogen bonded to O2P and O5' of g17, skipping the bulged adenine a16 and stabilizing the sugar-phosphate backbone of the hybrid. The hydrogen bonding and the backbone conformation at the bulged adenine site is very similar to that found in the crystal structure of a protein-RNA complex.
| + | |
| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1EFO 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=1EFO OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag)., Sudarsanakumar C, Xiong Y, Sundaralingam M, J Mol Biol. 2000 May 26;299(1):103-12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10860725 10860725]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Sudarsanakumar, C.]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: Xiong, Y.]] | + | |
| - | [[Category: a-form conformation]]
| + | |
| - | [[Category: adenine bulge]]
| + | |
| - | [[Category: hybrid]]
| + | |
| - | [[Category: looped out]]
| + | |
| - | [[Category: x-ray structure]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:01:32 2008''
| + | |
