1r7w
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1r7w |SIZE=350|CAPTION= <scene name='initialview01'>1r7w</scene> | |PDB= 1r7w |SIZE=350|CAPTION= <scene name='initialview01'>1r7w</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</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=[[1r7z|1R7Z]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r7w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r7w OCA], [http://www.ebi.ac.uk/pdbsum/1r7w PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1r7w RCSB]</span> | ||
}} | }} | ||
| Line 29: | Line 32: | ||
[[Category: stem-and-loop structure]] | [[Category: stem-and-loop structure]] | ||
| - | ''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 23:24:26 2008'' |
Revision as of 20:24, 30 March 2008
| |||||||
| Ligands: | , , , | ||||||
| Related: | 1R7Z
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
NMR STRUCTURE OF THE R(GGAGGACAUCCCUCACGGGUGACCGUGGUCCUCC), DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES WITH AUCCCU BULGE
Overview
The 5'-untranslated region of positive-strand RNA viruses harbors many cis-acting RNA structural elements that are important for various viral processes such as replication, translation, and packaging of new virions. Among these is loop B RNA of the stem-loop IV domain within the internal ribosomal entry site (IRES) of enteroviruses, including Poliovirus type 1 (PV1). Studies on PV1 have shown that specific recognition of loop B by the first KH (hnRNP K homology) domain of cellular poly(rC)-binding protein 2 (PCBP2) is essential for efficient translation of the viral mRNA. Here we report the NMR solution structures of two representative sequence variants of enteroviral loop B RNA. The two RNA variants differ at only one position (C vs U) within a six-nucleotide asymmetric internal loop sequence that is the binding site for the PCBP2 KH1 domain. Surprisingly, the two RNAs are drastically different in the overall shape and local dynamics of the bulge region. The RNA with the 5'-AUCCCU bulge sequence adopts an overall L shape. Its bulge nucleotides, especially the last four, are highly flexible and not very well defined by NMR. The RNA with the 5'-AUUCCU bulge sequence adopts an overall U shape, and its bulge sequence exhibits only limited flexibility. A detailed analysis of the two RNA structures and their dynamic properties, as well as available sequence data and known KH domain-RNA complex structures, not only provides insights into how loop B RNA might be recognized by the PCBP2 KH1 domain but also suggests a possible correlation between structural flexibility and pre-existing structural features for protein recognition.
About this Structure
1R7W is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus internal ribosome entry site: a single C to U substitution drastically changes the shape and flexibility of RNA., Du Z, Ulyanov NB, Yu J, Andino R, James TL, Biochemistry. 2004 May 18;43(19):5757-71. PMID:15134450
Page seeded by OCA on Sun Mar 30 23:24:26 2008
