2tpk

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[[Image:2tpk.jpg|left|200px]]
[[Image:2tpk.jpg|left|200px]]
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{{Structure
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|PDB= 2tpk |SIZE=350|CAPTION= <scene name='initialview01'>2tpk</scene>
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The line below this paragraph, containing "STRUCTURE_2tpk", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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{{STRUCTURE_2tpk| PDB=2tpk | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2tpk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2tpk OCA], [http://www.ebi.ac.uk/pdbsum/2tpk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2tpk RCSB]</span>
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'''AN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GENE 32 MESSENGER RNA OF BACTERIOPHAGE T2 USING HETERONUCLEAR NMR METHODS'''
'''AN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GENE 32 MESSENGER RNA OF BACTERIOPHAGE T2 USING HETERONUCLEAR NMR METHODS'''
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==About this Structure==
==About this Structure==
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2TPK 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=2TPK OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2TPK OCA].
==Reference==
==Reference==
An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2., Holland JA, Hansen MR, Du Z, Hoffman DW, RNA. 1999 Feb;5(2):257-71. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10024177 10024177]
An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2., Holland JA, Hansen MR, Du Z, Hoffman DW, RNA. 1999 Feb;5(2):257-71. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10024177 10024177]
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[[Category: Protein complex]]
 
[[Category: Du, Z.]]
[[Category: Du, Z.]]
[[Category: Hansen, M R.]]
[[Category: Hansen, M R.]]
[[Category: Hoffman, D W.]]
[[Category: Hoffman, D W.]]
[[Category: Holland, J A.]]
[[Category: Holland, J A.]]
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[[Category: pseudoknot]]
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[[Category: Pseudoknot]]
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[[Category: ribonucleic acid]]
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[[Category: Ribonucleic acid]]
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[[Category: rna]]
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[[Category: Rna]]
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[[Category: t2]]
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[[Category: T2]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 17:25:40 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:03:59 2008''
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Revision as of 14:25, 4 May 2008

Image:2tpk.jpg

Template:STRUCTURE 2tpk

AN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GENE 32 MESSENGER RNA OF BACTERIOPHAGE T2 USING HETERONUCLEAR NMR METHODS


Overview

The RNA pseudoknot located at the 5' end of the gene 32 messenger RNA of bacteriophage T2 contains two A-form helical stems connected by two loops, in an H-type pseudoknot topology. A combination of multidimensional NMR methods and isotope labeling were used to investigate the pseudoknot structure, resulting in a more detailed structural model than provided by earlier homonuclear NMR studies. Of particular significance, the interface between the stacked helical stems within the pseudoknot motif is described in detail. The two stems are stacked in a coaxial manner, with an approximately 18 degrees rotation of stem1 relative to stem2 about an axis that is parallel to the helical axis. This rotation serves to relieve what would otherwise be a relatively close phosphate-phosphate contact at the junction of the two stems, while preserving the stabilizing effects of base stacking. The ability of the NMR data to determine pseudoknot bending was critically assessed. The data were found to be a modestly precise indicator of pseudoknot bending, with the angle between the helical axes of stem1 and stem2 being in the range of 15+/-15 degrees. Pseudoknot models with bend angles within this range are equally consistent with the data, since they differ by only small amounts in the relatively short-range interproton distances from which the structure was derived. The gene 32 messenger RNA pseudoknot was compared with other RNA structures with coaxial or near-coaxial stacked helical stems.

About this Structure

Full crystallographic information is available from OCA.

Reference

An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2., Holland JA, Hansen MR, Du Z, Hoffman DW, RNA. 1999 Feb;5(2):257-71. PMID:10024177 Page seeded by OCA on Sun May 4 17:25:40 2008

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