1pbm
From Proteopedia
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|PDB= 1pbm |SIZE=350|CAPTION= <scene name='initialview01'>1pbm</scene> | |PDB= 1pbm |SIZE=350|CAPTION= <scene name='initialview01'>1pbm</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1pbl|1PBL]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pbm OCA], [http://www.ebi.ac.uk/pdbsum/1pbm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pbm RCSB]</span> | ||
}} | }} | ||
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[[Category: rna duplex]] | [[Category: rna duplex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:57:33 2008'' |
Revision as of 19:57, 30 March 2008
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| Ligands: | , | ||||||
| Related: | 1PBL
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF RIBONUCLEIC ACID, NMR, 1 STRUCTURE
Overview
Structures of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 have been determined by NMR spectroscopy under low salt conditions. All protons and phosphorus nuclei resonances have been assigned. Signals of H5'/5" have been assigned stereospecifically. All 3JH,H and 3JP,H coupling constants have been measured. The structures were determined and refined using an iterative relaxation matrix procedure (IRMA) and the restrained MD simulation. Both duplexes form half-turn, right-handed helices with several conformational features which deviate significantly from a canonical A-RNA structure. Duplexes are characterised as having C3'-endo sugar pucker, very low base-pair rise and high helical twist and inclination angles. Helices are overwound with <10 bp per turn. There is limited inter-strand guanine stacking for CG steps. Within CG steps of both duplexes, the planes of the inter-strand cytosines are not parallel while guanines are almost parallel. For the GC steps this pattern is reversed. The 2'-O-methyl groups are spatially close to the 5'-hydrogens of neighbouring residues from the 3'-side and are directed towards the minor groove of 2'-O-Me(CGCGCG)2 forming a hydrophobic layer. Solution structures of both duplexes are similar; the effect of 2'-O-methylation on the parent RNA structure is small. This suggests that intrinsic properties imposed by alternating CG base pairs govern the overall conformation of both duplexes.
About this Structure
1PBM is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions., Popenda M, Biala E, Milecki J, Adamiak RW, Nucleic Acids Res. 1997 Nov 15;25(22):4589-98. PMID:9358170
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