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.


310d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:25, 21 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:310d.jpg|left|200px]]
 
-
{{Structure
+
==Crystal structure of 2'-O-Me(CGCGCG)2: an RNA duplex at 1.3 A resolution. Hydration pattern of 2'-O-methylated RNA==
-
|PDB= 310d |SIZE=350|CAPTION= <scene name='initialview01'>310d</scene>, resolution 1.300&Aring;
+
<StructureSection load='310d' size='340' side='right'caption='[[310d]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
+
<table><tr><td colspan='2'>[[310d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=310D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=310D FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene></td></tr>
-
}}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=310d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=310d OCA], [https://pdbe.org/310d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=310d RCSB], [https://www.ebi.ac.uk/pdbsum/310d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=310d ProSAT]</span></td></tr>
-
 
+
</table>
-
'''CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.3 A RESOLUTION. HYDRATION PATTERN OF 2'-O-METHYLATED RNA'''
+
__TOC__
-
 
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
==Overview==
+
[[Category: Synthetic construct]]
-
The molecular and crystal structure of 2'-O-Me (CGCGCG)2 has been determined using synchrotron radiation at near-atomic resolution (1.30 A), the highest resolution to date in the RNA field. The crystal structure is a half-turn A-type helix with some helical parameters deviating from canonical A-RNA, such as low base pair rise, elevated helical twist and inclination angles. In CG steps, inter-strand guanines are parallel while cytosines are not parallel. In steps GC this motif is reversed. This type of regularity is not seen in other RNA crystal structures. The structure includes 44 water molecules and two hydrated Mg2+ions one of which lies exactly on the crystallographic 2-fold axis. There are distinct patterns of hydration in the major and the minor grooves. The major groove is stabilised by water clusters consisting of fused five- and six-membered rings. Minor groove contains only a single row of water molecules; each water bridges either two self-parallel cytosines or two self-parallel guanines by a pair of hydrogen bonds. The structure provides the first view of the hydration scheme of 2'-O-methylated RNA duplex.
+
[[Category: Adamiak DA]]
-
 
+
[[Category: Adamiak RW]]
-
==About this Structure==
+
[[Category: Dauter Z]]
-
310D 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=310D OCA].
+
[[Category: Milecki J]]
-
 
+
[[Category: Rypniewski WR]]
-
==Reference==
+
-
Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA., Adamiak DA, Milecki J, Popenda M, Adamiak RW, Dauter Z, Rypniewski WR, Nucleic Acids Res. 1997 Nov 15;25(22):4599-607. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9358171 9358171]
+
-
[[Category: Protein complex]]
+
-
[[Category: Adamiak, D A.]]
+
-
[[Category: Adamiak, R W.]]
+
-
[[Category: Dauter, Z.]]
+
-
[[Category: Milecki, J.]]
+
-
[[Category: Rypniewski, W R.]]
+
-
[[Category: MG]]
+
-
[[Category: a-rna]]
+
-
[[Category: double helix]]
+
-
[[Category: modified]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:54:26 2008''
+

Current revision

Crystal structure of 2'-O-Me(CGCGCG)2: an RNA duplex at 1.3 A resolution. Hydration pattern of 2'-O-methylated RNA

PDB ID 310d

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/310d"
Personal tools