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307d

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[[Image:307d.gif|left|200px]]
 
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==Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis==
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The line below this paragraph, containing "STRUCTURE_307d", creates the "Structure Box" on the page.
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<StructureSection load='307d' size='340' side='right'caption='[[307d]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[307d]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=307D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=307D FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=307d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=307d OCA], [https://pdbe.org/307d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=307d RCSB], [https://www.ebi.ac.uk/pdbsum/307d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=307d ProSAT]</span></td></tr>
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{{STRUCTURE_307d| PDB=307d | SCENE= }}
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</table>
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__TOC__
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'''STRUCTURE OF A DNA ANALOG OF THE PRIMER FOR HIV-1 RT SECOND STRAND SYNTHESIS'''
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Cascio D]]
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==Overview==
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[[Category: Dickerson RE]]
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The non-self-complementary DNA decamer C-A-A-A-G-A-A-A-A-G/C-T-T-T-T-C-T-T-T-G is a DNA/DNA analogue of a portion of the polypurine tract or PPT, which is a RNA/DNA hybrid that serves as a primer for synthesis of the (+) DNA strand by HIV reverse transcriptase (RT), and which is not digested by the RNase H domain of reverse transcriptase following (-) strand synthesis. The same unusual conformation that eludes RNase H, thought to be a change in width of minor groove, may also be responsible for the inhibition of HIV RT by minor groove binding drugs such as distamycin and their bis-linked derivatives. The present X-ray crystal structure of this DNA decamer exhibits the usual properties of A-tract B-DNA under biologically relevant conditions: large propeller twist of base-pairs, narrowed minor groove, and a straight helix axis. Groove narrowing is fully developed in the A-A-A-A region, but not in the A-A-A region, which previous investigators have proposed as being too short to exhibit typical A-tract properties. The RNA/DNA hybrid produced by HIV reverse transcriptase during (-) strand synthesis presumably forms a "heteromerous" or H-helix with narrower minor groove than an A-helical RNA/RNA duplex. If the narrowing of minor groove in A-tract H-helices is comparable to that seen in A-tract B-helices, then the narrowed minor groove of the polypurine tract could make the second primer site both (1) impervious to RNase H digestion, and (2) susceptible to inhibition by minor groove binding drugs.
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[[Category: Grzeskowiak K]]
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[[Category: Han GW]]
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==About this Structure==
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[[Category: Kopka ML]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=307D OCA].
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==Reference==
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Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis., Han GW, Kopka ML, Cascio D, Grzeskowiak K, Dickerson RE, J Mol Biol. 1997 Jun 27;269(5):811-26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9223643 9223643]
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[[Category: Cascio, D.]]
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[[Category: Dickerson, R E.]]
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[[Category: Grzeskowiak, K.]]
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[[Category: Han, G W.]]
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[[Category: Kopka, M L.]]
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[[Category: B-dna]]
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[[Category: Double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 20:14:54 2008''
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Current revision

Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis

PDB ID 307d

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