1et4
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1et4 |SIZE=350|CAPTION= <scene name='initialview01'>1et4</scene>, resolution 2.30Å | |PDB= 1et4 |SIZE=350|CAPTION= <scene name='initialview01'>1et4</scene>, resolution 2.30Å | ||
|SITE= <scene name='pdbsite=1:Groove+Binder'>1</scene> | |SITE= <scene name='pdbsite=1:Groove+Binder'>1</scene> | ||
| - | |LIGAND= <scene name='pdbligand=CNC:CO-CYANOCOBALAMIN'>CNC</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CNC:CO-CYANOCOBALAMIN'>CNC</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1ddy|1DDY]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1et4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1et4 OCA], [http://www.ebi.ac.uk/pdbsum/1et4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1et4 RCSB]</span> | ||
}} | }} | ||
| Line 23: | Line 26: | ||
[[Category: Sussman, D.]] | [[Category: Sussman, D.]] | ||
[[Category: Wilson, C.]] | [[Category: Wilson, C.]] | ||
| - | [[Category: CNC]] | ||
[[Category: b12 binding rna]] | [[Category: b12 binding rna]] | ||
[[Category: cobalamin]] | [[Category: cobalamin]] | ||
| Line 29: | Line 31: | ||
[[Category: vitamin b12]] | [[Category: vitamin b12]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:09:08 2008'' |
Revision as of 17:09, 30 March 2008
| |||||||
| , resolution 2.30Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , , , | ||||||
| Related: | 1DDY
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF A VITAMIN B12 BINDING RNA APTAMER WITH LIGAND AT 2.3 A
Overview
BACKGROUND: The 3.0 A crystal structure of the vitamin B(12) RNA aptamer revealed an unusual tertiary structure that is rich in novel RNA structural motifs. Important details of the interactions that stabilize noncanonical base pairing and the role of solvent in the structure were not apparent owing to the limited resolution. RESULTS: The structure of the vitamin B(12) RNA aptamer in complex with its ligand has been determined at 2.3 A resolution by X-ray crystallography. The crystallographic asymmetric unit contains five independent copies of the aptamer-vitamin B(12) complex, making it possible to accurately define well-conserved features. The core of the aptamer contains an unusual water-filled channel that is buried between the three strands of an RNA triplex. Well-ordered water molecules positioned within this channel form bridging hydrogen bonds and stabilize planar base triples that otherwise lack significant direct base-base contacts. The water channel terminates at the interface between the RNA and the bound ligand, leaving a pair of water molecules appropriately positioned to hydrogen bond with the highly polarized cyanide nitrogen of vitamin B(12). Analysis of the general solvation patterns for each nucleotide suggests that water molecules are not precisely positioned, as observed in previous RNA duplex structures, but instead might adjust in response to the varying local environment. Unusual intermolecular base pairing contributes to the formation of three different dimerization contacts that drive formation of the crystal lattice. CONCLUSIONS: The structure demonstrates the important role of water molecules and noncanonical base pairing in driving the formation of RNA tertiary structure and facilitating specific interactions of RNAs with other molecules.
About this Structure
1ET4 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
A water channel in the core of the vitamin B(12) RNA aptamer., Sussman D, Wilson C, Structure. 2000 Jul 15;8(7):719-27. PMID:10903943
Page seeded by OCA on Sun Mar 30 20:09:08 2008
