This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1g4q
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:1g4q.gif|left|200px]] | [[Image:1g4q.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_1g4q", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{STRUCTURE_1g4q| PDB=1g4q | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG''' | '''RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG''' | ||
| Line 19: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. | |
==Reference== | ==Reference== | ||
Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11173466 11173466] | Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11173466 11173466] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Han, G W.]] | [[Category: Han, G W.]] | ||
| - | [[Category: | + | [[Category: Direct method]] |
| - | [[Category: | + | [[Category: Polypurine tract of hiv-1]] |
| - | [[Category: | + | [[Category: Rna/dna hybrid]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 17:08:14 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 14:08, 2 May 2008
RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG
Overview
For the first time, ab initio direct methods have been used to solve the crystal structure of an RNA/DNA hybrid decamer. The RNA/DNA sequence corresponds to the leftmost two-thirds of the polypurine tract (PPT), the primer for second-strand DNA synthesis by HIV-1 reverse transcriptase (RT). Direct methods using Shake-and-Bake (SnB) yielded solutions for the RNA/DNA decamer molecule using 1.15 A data, which is just on the resolution edge of what might work with direct methods. Atomic positions for 96% of the entire molecule, containing 514 non-H atoms including three Ca(2+) ions, were easily interpreted from a Fourier map based on the 'Shake-and-Bake' minimal function and CROQUE phase-refinement program. Only six atoms, primarily in the sugar linkage, were missing in this Fourier map. At present, the R factor of the model is 0.143 (R(free) = 0.186) for the 562 non-H atom sites located. The conformation of the RNA/DNA helix is A-form, with a typical A-helix minor-groove width. This paper presents the methodology used in solving this structure.
About this Structure
Full crystallographic information is available from OCA.
Reference
Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:11173466 Page seeded by OCA on Fri May 2 17:08:14 2008
