1qc0
From Proteopedia
(New page: 200px<br /><applet load="1qc0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qc0, resolution 1.55Å" /> '''CRYSTAL STRUCTURE OF...) |
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| - | [[Image:1qc0.gif|left|200px]]<br /><applet load="1qc0" size=" | + | [[Image:1qc0.gif|left|200px]]<br /><applet load="1qc0" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1qc0, resolution 1.55Å" /> | caption="1qc0, resolution 1.55Å" /> | ||
'''CRYSTAL STRUCTURE OF A 19 BASE PAIR COPY CONTROL RELATED RNA DUPLEX'''<br /> | '''CRYSTAL STRUCTURE OF A 19 BASE PAIR COPY CONTROL RELATED RNA DUPLEX'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structures of two RNA duplexes, whose sequences correspond to portions | + | The structures of two RNA duplexes, whose sequences correspond to portions of the ColE1 plasmid copy control RNA I and RNA II, have been determined. Crystals containing the 18mers 5'-CA CCGUUGGUAGCGGUGC-3' and 5'-CACCGCUACCAACGGUGC-3' diffract to 1.20 A resolution while those containing the 19mers 5'-GCACCGUUGGUAGCGGUGC-3' and 5'-GCACCGCUACCAACGGUGC-3' diffract to 1.55 A resolution. Both duplexes are standard A form, with Watson-Crick base pairing throughout. Use of anisotropic atomic displacement factors in refinement of the 1.20 A structure dramatically improved refinement statistics, resulting in a final R(free) of 15.0% and a crystallographic R-factor of 11.6%. Perhaps surprisingly, these crystals of the 18 base pair RNA exhibit a 36-fold static disorder, resulting in a structure with a single sugar-phosphate backbone conformation and an averaged base composition at each residue. Since the sugar-phosphate backbone structure is identical in the 36 different nucleotides that are superimposed, there can be no sequence-dependent variation in the structure. The average ribose pucker amplitude is 45.8 degrees for the 18 base pair structure and 46.4 degrees for the 19 base pair structure; these values are respectively 19% and 20% larger than the average pucker amplitude reported from nucleoside crystal structures. A standard RNA water structure, based on analysis of the hydration of these crystal structures and that of the TAR RNA stem [Ippolito, J. A., and Steitz, T. A. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 9819-9824], has been derived, which has allowed us to predict water positions in lower resolution RNA crystal structures. We report a new RNA packing motif, in which three pro-S(p) phosphate oxygens interact with an ammonium ion. |
==About this Structure== | ==About this Structure== | ||
| - | 1QC0 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NH4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1QC0 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NH4:'>NH4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QC0 OCA]. |
==Reference== | ==Reference== | ||
Crystal structures of two plasmid copy control related RNA duplexes: An 18 base pair duplex at 1.20 A resolution and a 19 base pair duplex at 1.55 A resolution., Klosterman PS, Shah SA, Steitz TA, Biochemistry. 1999 Nov 9;38(45):14784-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10555960 10555960] | Crystal structures of two plasmid copy control related RNA duplexes: An 18 base pair duplex at 1.20 A resolution and a 19 base pair duplex at 1.55 A resolution., Klosterman PS, Shah SA, Steitz TA, Biochemistry. 1999 Nov 9;38(45):14784-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10555960 10555960] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Klosterman, P | + | [[Category: Klosterman, P S.]] |
| - | [[Category: Shah, S | + | [[Category: Shah, S A.]] |
| - | [[Category: Steitz, T | + | [[Category: Steitz, T A.]] |
[[Category: NH4]] | [[Category: NH4]] | ||
[[Category: a-rna structure]] | [[Category: a-rna structure]] | ||
[[Category: ribonucleic acid]] | [[Category: ribonucleic acid]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:38:04 2008'' |
Revision as of 12:38, 21 February 2008
|
CRYSTAL STRUCTURE OF A 19 BASE PAIR COPY CONTROL RELATED RNA DUPLEX
Overview
The structures of two RNA duplexes, whose sequences correspond to portions of the ColE1 plasmid copy control RNA I and RNA II, have been determined. Crystals containing the 18mers 5'-CA CCGUUGGUAGCGGUGC-3' and 5'-CACCGCUACCAACGGUGC-3' diffract to 1.20 A resolution while those containing the 19mers 5'-GCACCGUUGGUAGCGGUGC-3' and 5'-GCACCGCUACCAACGGUGC-3' diffract to 1.55 A resolution. Both duplexes are standard A form, with Watson-Crick base pairing throughout. Use of anisotropic atomic displacement factors in refinement of the 1.20 A structure dramatically improved refinement statistics, resulting in a final R(free) of 15.0% and a crystallographic R-factor of 11.6%. Perhaps surprisingly, these crystals of the 18 base pair RNA exhibit a 36-fold static disorder, resulting in a structure with a single sugar-phosphate backbone conformation and an averaged base composition at each residue. Since the sugar-phosphate backbone structure is identical in the 36 different nucleotides that are superimposed, there can be no sequence-dependent variation in the structure. The average ribose pucker amplitude is 45.8 degrees for the 18 base pair structure and 46.4 degrees for the 19 base pair structure; these values are respectively 19% and 20% larger than the average pucker amplitude reported from nucleoside crystal structures. A standard RNA water structure, based on analysis of the hydration of these crystal structures and that of the TAR RNA stem [Ippolito, J. A., and Steitz, T. A. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 9819-9824], has been derived, which has allowed us to predict water positions in lower resolution RNA crystal structures. We report a new RNA packing motif, in which three pro-S(p) phosphate oxygens interact with an ammonium ion.
About this Structure
1QC0 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Crystal structures of two plasmid copy control related RNA duplexes: An 18 base pair duplex at 1.20 A resolution and a 19 base pair duplex at 1.55 A resolution., Klosterman PS, Shah SA, Steitz TA, Biochemistry. 1999 Nov 9;38(45):14784-92. PMID:10555960
Page seeded by OCA on Thu Feb 21 14:38:04 2008
