1nxr

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[[Image:1nxr.gif|left|200px]]
[[Image:1nxr.gif|left|200px]]
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{{Structure
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|PDB= 1nxr |SIZE=350|CAPTION= <scene name='initialview01'>1nxr</scene>
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The line below this paragraph, containing "STRUCTURE_1nxr", creates the "Structure Box" on the page.
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|SITE=
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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=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</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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|ACTIVITY=
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{{STRUCTURE_1nxr| PDB=1nxr | 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=1nxr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nxr OCA], [http://www.ebi.ac.uk/pdbsum/1nxr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nxr RCSB]</span>
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'''HIV-1 POLYPURINE HYBRID, R(GAGGACUG):D(CAGTCCTC), NMR, 18 STRUCTURES'''
'''HIV-1 POLYPURINE HYBRID, R(GAGGACUG):D(CAGTCCTC), NMR, 18 STRUCTURES'''
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==About this Structure==
==About this Structure==
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1NXR 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=1NXR OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NXR OCA].
==Reference==
==Reference==
Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1 (+)-strand synthesis., Fedoroff OY, Ge Y, Reid BR, J Mol Biol. 1997 Jun 6;269(2):225-39. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9191067 9191067]
Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1 (+)-strand synthesis., Fedoroff OY, Ge Y, Reid BR, J Mol Biol. 1997 Jun 6;269(2):225-39. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9191067 9191067]
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[[Category: Protein complex]]
 
[[Category: Fedoroff, O Y.]]
[[Category: Fedoroff, O Y.]]
[[Category: Ge, Y.]]
[[Category: Ge, Y.]]
[[Category: Reid, B R.]]
[[Category: Reid, B R.]]
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[[Category: hiv-1 polypurine hybrid]]
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[[Category: Hiv-1 polypurine hybrid]]
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[[Category: reverse transcriptase]]
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[[Category: Reverse transcriptase]]
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[[Category: rna/dna hybrid]]
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[[Category: Rna/dna hybrid]]
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[[Category: rnase h]]
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[[Category: Rnase h]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 03:06:30 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:37:02 2008''
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Revision as of 00:06, 3 May 2008

Image:1nxr.gif

Template:STRUCTURE 1nxr

HIV-1 POLYPURINE HYBRID, R(GAGGACUG):D(CAGTCCTC), NMR, 18 STRUCTURES


Overview

The three-dimensional solution structure of the hybrid duplex r(gaggacug):d(CAGTCCTC) has been determined by two-dimensional NMR, distance geometry (DG), restrained molecular dynamics (rMD) and NOE back-calculation methods. This hybrid, consisting of a purine-rich RNA strand and a pyrimidine-rich DNA strand, is related to the polypurine (+)-strand primer formed after (-)-strand DNA synthesis and RNase H degradation of the viral RNA strand and contains the site of a specific cleavage by reverse transcription (RT) RNase H at the end of the HIV-1 polypurine tract. This polypurine primer is an important intermediate in the formation of virally encoded double-stranded DNA prior to HIV-1 retrovirus integration. The correct processing of this primer is vital in the life cycle of the human immunodeficiency virus type (HIV-1) retrovirus. The structure of the r(gaggacug):d(CAGTCCTC) hybrid, as determined in solution by NMR, is intermediate between canonical A-type and B-type double helices, and has mixed structural characteristics. It is quantitatively different from the previously determined solution structures of other RNA-DNA hybrids, particularly in the width and shape of the major groove, which is wider than the major groove of other hybrids and is close to the dimension of the major groove of B-type DNA duplexes. The structure of this hybrid duplex contains a prominent bend in the double helix with a magnitude and direction similar to the bend in Okazaki fragments. The structural features of the present duplex may explain the unique interactions of this sequence with HIV-1 RT during both (-)-strand and (+)-strand DNA synthesis.

About this Structure

Full crystallographic information is available from OCA.

Reference

Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1 (+)-strand synthesis., Fedoroff OY, Ge Y, Reid BR, J Mol Biol. 1997 Jun 6;269(2):225-39. PMID:9191067 Page seeded by OCA on Sat May 3 03:06:30 2008

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