1c4l: Difference between revisions
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|PDB= 1c4l |SIZE=350|CAPTION= <scene name='initialview01'>1c4l</scene> | |PDB= 1c4l |SIZE=350|CAPTION= <scene name='initialview01'>1c4l</scene> | ||
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1c4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c4l OCA], [http://www.ebi.ac.uk/pdbsum/1c4l PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1c4l RCSB]</span> | |||
}} | }} | ||
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[[Category: c-u base pair]] | [[Category: c-u base pair]] | ||
''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 19:14:22 2008'' | ||
Revision as of 16:14, 30 March 2008
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| 1c4l | |||||||||||||
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| Ligands: | A, C, G, U | ||||||||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
SOLUTION STRUCTURE OF AN RNA DUPLEX INCLUDING A C-U BASE-PAIR
Overview
The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of (15)N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solution structure of the RNA oligomer, r[CGACUCAGG].r[CCUGCGUCG], it was found that a single C-U mismatch preferred being stacked in the duplex rather than being flipped-out even in solution. Moreover, it adopts an irregular geometry, where the amino nitrogen (N4) of the cytidine and keto-oxygen (O4) of the uridine are within hydrogen-bonding distance, as seen in crystals. To further prove the presence of a hydrogen bond in the C-U pair, we employed a point-labeled cytidine at the exocyclic amino nitrogen of the cytidine in the C-U pair. The temperature profile of its (15)N chemical shift showed a sigmoidal transition curve, indicating the presence of a hydrogen bond in the C-U pair in the duplex.
About this Structure
1C4L is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of an RNA duplex including a C-U base pair., Tanaka Y, Kojima C, Yamazaki T, Kodama TS, Yasuno K, Miyashita S, Ono A, Ono A, Kainosho M, Kyogoku Y, Biochemistry. 2000 Jun 20;39(24):7074-80. PMID:10852704
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