1nem

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[[Image:1nem.gif|left|200px]]<br /><applet load="1nem" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1nem.gif|left|200px]]
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caption="1nem" />
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'''Saccharide-RNA recognition in the neomycin B / RNA aptamer complex'''<br />
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{{Structure
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|PDB= 1nem |SIZE=350|CAPTION= <scene name='initialview01'>1nem</scene>
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|SITE=
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|LIGAND= <scene name='pdbligand=BDG:O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE'>BDG</scene> and <scene name='pdbligand=NEB:2-DEOXY-D-STREPTAMINE'>NEB</scene>
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|ACTIVITY=
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|GENE=
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}}
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'''Saccharide-RNA recognition in the neomycin B / RNA aptamer complex'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1NEM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=BDG:'>BDG</scene> and <scene name='pdbligand=NEB:'>NEB</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEM OCA].
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1NEM 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=1NEM OCA].
==Reference==
==Reference==
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Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer., Jiang L, Majumdar A, Hu W, Jaishree TJ, Xu W, Patel DJ, Structure. 1999 Jul 15;7(7):817-27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10425683 10425683]
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Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer., Jiang L, Majumdar A, Hu W, Jaishree TJ, Xu W, Patel DJ, Structure. 1999 Jul 15;7(7):817-27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10425683 10425683]
[[Category: Protein complex]]
[[Category: Protein complex]]
[[Category: Hu, W.]]
[[Category: Hu, W.]]
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[[Category: rna aptamer]]
[[Category: rna aptamer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:05:15 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:55:50 2008''

Revision as of 10:55, 20 March 2008

Image:1nem.gif


PDB ID 1nem

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Ligands: and
Coordinates: save as pdb, mmCIF, xml



Saccharide-RNA recognition in the neomycin B / RNA aptamer complex


Overview

BACKGROUND: Aminoglycoside antibiotics can target RNA folds with micromolar affinity and inhibit biological processes ranging from protein biosynthesis to ribozyme action and viral replication. Specific features of aminoglycoside antibiotic-RNA recognition have been probed using chemical, biochemical, spectroscopic and computational approaches on both natural RNA targets and RNA aptamers identified through in vitro selection. Our previous studies on tobramycin-RNA aptamer complexes are extended to neomycin B bound to its selected RNA aptamer with 100 nM affinity. RESULTS: The neamine moiety (rings I and II) of neomycin B is sandwiched between the major groove floor of a 'zippered-up' G.U mismatch aligned segment and a looped-out purine base that flaps over the bound antibiotic. Specific intermolecular hydrogen bonds are observed between the charged amines of neomycin B and base mismatch edges and backbone phosphates. These interactions anchor 2-deoxystreptamine ring I and pyranose ring II within the RNA-binding pocket. CONCLUSIONS: The RNA aptamer complexes with tobramycin and neomycin B utilize common architectural principles to generate RNA-binding pockets for the bound aminoglycoside antibiotics. In each case, the 2-deoxystreptamine ring I and an attached pyranose ring are encapsulated within the major groove binding pocket, which is lined with mismatch pairs. The bound antibiotic within the pocket is capped over by a looped-out base and anchored in place through intermolecular hydrogen bonds involving charged amine groups of the antibiotic.

About this Structure

1NEM is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer., Jiang L, Majumdar A, Hu W, Jaishree TJ, Xu W, Patel DJ, Structure. 1999 Jul 15;7(7):817-27. PMID:10425683

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