Related ArticlesNMR 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.
Biochemistry. 2004 May 18;43(19):5757-71
Authors: Du Z, Ulyanov NB, Yu J, Andino R, James TL
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.
[NMR paper] NMR structure of the 3' stem-loop from human U4 snRNA.
NMR structure of the 3' stem-loop from human U4 snRNA.
Related Articles NMR structure of the 3' stem-loop from human U4 snRNA.
Nucleic Acids Res. 2002 Oct 15;30(20):4371-9
Authors: Comolli LR, Ulyanov NB, Soto AM, Marky LA, James TL, Gmeiner WH
The NMR structure of the 3' stem-loop (3'SL) from human U4 snRNA was determined to gain insight into the structural basis for conservation of this stem-loop sequence from vertebrates. 3'SL sequences from human, rat, mouse and chicken U4 snRNA each consist of a 7 bp stem capped by a UACG tetraloop. No...
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[NMR paper] NMR structure of the second intracellular loop of the alpha 2A adrenergic receptor: e
NMR structure of the second intracellular loop of the alpha 2A adrenergic receptor: evidence for a novel cytoplasmic helix.
Related Articles NMR structure of the second intracellular loop of the alpha 2A adrenergic receptor: evidence for a novel cytoplasmic helix.
Biochemistry. 2002 Mar 19;41(11):3596-604
Authors: Chung DA, Zuiderweg ER, Fowler CB, Soyer OS, Mosberg HI, Neubig RR
A major, unresolved question in signal transduction by G protein coupled receptors (GPCRs) is to understand how, at atomic resolution, a GPCR activates a G protein. A...
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[NMR paper] NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop bin
NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein.
Related Articles NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein.
RNA. 2002 Jan;8(1):83-96
Authors: DeJong ES, Marzluff WF, Nikonowicz EP
The 3' end of replication-dependent histone mRNAs terminate in a conserved sequence containing a stem-loop. This 26-nt sequence is the binding site for a protein, stem-loop binding protein (SLBP), that is involved in multiple aspects of histone mRNA metabolism...
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[NMR paper] NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA
NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition.
Related Articles NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition.
J Mol Biol. 2000 Aug 11;301(2):491-511
Authors: Amarasinghe GK, De Guzman RN, Turner RB, Chancellor KJ, Wu ZR, Summers MF
The RNA genome of the human immunodeficiency virus type-1 (HIV-1) contains a approximately 120 nucleotide Psi-packaging signal...
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[NMR paper] NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel
NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform.
Related Articles NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform.
J Mol Biol. 2000 May 26;299(1):145-56
Authors: Amarasinghe GK, De Guzman RN, Turner RB, Summers MF
The genome of the human immunodeficiency virus type-1 (HIV-1) contains a stretch of approximately 120 nucleotides known as the psi-site that is essential for RNA packaging during virus assembly. These...
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[NMR paper] Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR
Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry.
Biochemistry. 1997 Nov 18;36(46):13989-4002
Authors: Sich C, Ohlenschläger O, Ramachandran R, Görlach M, Brown LR
Structural features of a 19-nucleotide RNA hairpin loop (5'-GGCGUACGUUUCGUACGCC-3'),...
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[NMR paper] The mobile loop region of the NAD(H) binding component (dI) of proton-translocating n
The mobile loop region of the NAD(H) binding component (dI) of proton-translocating nicotinamide nucleotide transhydrogenase from Rhodospirillum rubrum: complete NMR assignment and effects of bound nucleotides.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles The mobile loop region of the NAD(H) binding component (dI) of proton-translocating nicotinamide nucleotide transhydrogenase from Rhodospirillum rubrum: complete NMR assignment and effects of bound nucleotides.
Biochim Biophys Acta. 1999...
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[NMR paper] Solid-state NMR evidence for an antibody-dependent conformation of the V3 loop of HIV
Solid-state NMR evidence for an antibody-dependent conformation of the V3 loop of HIV-1 gp120.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.nature.com-images-lo_nsb.gif Related Articles Solid-state NMR evidence for an antibody-dependent conformation of the V3 loop of HIV-1 gp120.
Nat Struct Biol. 1999 Feb;6(2):141-5
Authors: Weliky DP, Bennett AE, Zvi A, Anglister J, Steinbach PJ, Tycko R
Solid-state NMR measurements have been carried out on frozen solutions of the complex of a 24-residue peptide derived from the third variable...
NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus interna
Linear Mode
