1drn

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
[[Image:1drn.jpg|left|200px]]
[[Image:1drn.jpg|left|200px]]
-
{{Structure
+
<!--
-
|PDB= 1drn |SIZE=350|CAPTION= <scene name='initialview01'>1drn</scene>
+
The line below this paragraph, containing "STRUCTURE_1drn", creates the "Structure Box" on the page.
-
|SITE=
+
You may change the PDB parameter (which sets the PDB file loaded into the applet)
-
|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>
+
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-
|ACTIVITY=
+
or leave the SCENE parameter empty for the default display.
-
|GENE=
+
-->
-
|DOMAIN=
+
{{STRUCTURE_1drn| PDB=1drn | SCENE= }}
-
|RELATEDENTRY=[[1dhh|1DHH]]
+
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1drn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1drn OCA], [http://www.ebi.ac.uk/pdbsum/1drn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1drn RCSB]</span>
+
-
}}
+
'''NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GGAGA)R(UGAC)/D(GTCATCTCC)'''
'''NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GGAGA)R(UGAC)/D(GTCATCTCC)'''
Line 19: Line 16:
==About this Structure==
==About this Structure==
-
1DRN 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=1DRN OCA].
+
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DRN OCA].
==Reference==
==Reference==
Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC)., Nishizaki T, Iwai S, Ohkubo T, Kojima C, Nakamura H, Kyogoku Y, Ohtsuka E, Biochemistry. 1996 Apr 2;35(13):4016-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8672435 8672435]
Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC)., Nishizaki T, Iwai S, Ohkubo T, Kojima C, Nakamura H, Kyogoku Y, Ohtsuka E, Biochemistry. 1996 Apr 2;35(13):4016-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8672435 8672435]
-
[[Category: Protein complex]]
 
[[Category: Iwai, S.]]
[[Category: Iwai, S.]]
[[Category: Kojima, C.]]
[[Category: Kojima, C.]]
Line 31: Line 27:
[[Category: Ohkubo, T.]]
[[Category: Ohkubo, T.]]
[[Category: Ohtsuka, E.]]
[[Category: Ohtsuka, E.]]
-
[[Category: dna/rna hybrid]]
+
[[Category: Dna/rna hybrid]]
-
[[Category: double helix]]
+
[[Category: Double helix]]
-
[[Category: nmr]]
+
[[Category: Nmr]]
-
 
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 14:11:38 2008''
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:47:25 2008''
+

Revision as of 11:11, 2 May 2008

Image:1drn.jpg

Template:STRUCTURE 1drn

NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GGAGA)R(UGAC)/D(GTCATCTCC)


Overview

The solution structures of two DNA duplexes containing a DNA*RNA hybrid region at different sites, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) (DHD, where D and H represent the DNA and DNA x RNA hybrid segments, respectively) and d(GGAGA)r(UGAC) x d(GTCATCTCC) (DDH), were determined by nuclear magnetic resonance spectroscopy to clarify the structural features of the D-H and H-D junctions. All proton-proton distances were derived from the NOESY spectra, with mixing times of 45 ms, and the restrained molecular dynamics were carried out starting from the typical A- and B-form conformations. Both duplexes were converged from the respective initial structures into structures with RMSD values of less than 1.0 angstrom. These structures were subjected to full relaxation matrix refinement to produce the final structures. In the case of the D-H junction, where the ribonucleotide was linked to the 3'-end of the DNA, the H2' and H2" signals of the deoxynucleotide overlapped completely, and the ribonucleotide had a H1'-H2' coupling constant larger than that of the normal C3'-endo sugar pucker. The dihedral angles, the pseudorotation phase angles, and the helical parameters changed at the H-D junction, but not at the D-H junction. A detailed comparison of the two duplexes revealed the structural heterogeneity between the DNA segment and the DNA x RNA hybrid region and the transitions at the junctions.

About this Structure

Full crystallographic information is available from OCA.

Reference

Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC)., Nishizaki T, Iwai S, Ohkubo T, Kojima C, Nakamura H, Kyogoku Y, Ohtsuka E, Biochemistry. 1996 Apr 2;35(13):4016-25. PMID:8672435 Page seeded by OCA on Fri May 2 14:11:38 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1drn"
Personal tools