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 high resolution structure has previously been reported for a UACG tetraloop. The UACG tetraloop portion of the 3'SL was especially well defined by the NMR data, with a total of 92 NOE-derived restraints (about 15 per residue), including 48 inter-residue restraints (about 8 per residue) for the tetraloop and closing C-G base pair. Distance restraints were derived from NOESY spectra using MARDIGRAS with random error analysis. Refinement of the 20mer RNA hairpin structure was carried out using the programs DYANA and miniCarlo. In the UACG tetraloop, U and G formed a base pair stabilized by two hydrogen bonds, one between the 2'-hydroxyl proton of U and carbonyl oxygen of G, another between the imino proton of G and carbonyl oxygen O2 of U. In addition, the amino group of C formed a hydrogen bond with the phosphate oxygen of A. G adopted a syn orientation about the glycosidic bond, while the sugar puckers of A and C were either C2'-endo or flexible. The conformation of the UACG tetraloop was, overall, similar to that previously reported for UUCG tetraloops, another member of the UNCG class of tetraloops. The presence of an A, rather than a U, at the variable position, however, presents a distinct surface for interaction of the 3'SL tetraloop with either RNA or protein residues that may stabilize interactions important for active spliceosome formation. Such tertiary interactions may explain the conservation of the UACG tetraloop motif in 3'SL sequences from U4 snRNA in vertebrates.
[NMR paper] NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus interna
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.
Related Articles 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.
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...
nmrlearner
Journal club
0
11-24-2010 09:51 PM
[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...
nmrlearner
Journal club
0
11-24-2010 08:49 PM
[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...
nmrlearner
Journal club
0
11-19-2010 08:29 PM
[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...
nmrlearner
Journal club
0
11-18-2010 09:15 PM
[NMR paper] NMR solution structure of a cytoplasmic surface loop of the human red cell anion tran
NMR solution structure of a cytoplasmic surface loop of the human red cell anion transporter, band 3.
Related Articles NMR solution structure of a cytoplasmic surface loop of the human red cell anion transporter, band 3.
Biochemistry. 1998 Aug 18;37(33):11670-8
Authors: Askin D, Bloomberg GB, Chambers EJ, Tanner MJ
The membrane domain of the human red cell anion transport protein, band 3, is too large to be studied by solution nuclear magnetic resonance spectroscopy (NMR), and its amphiphilic nature requires the use of detergents for...
nmrlearner
Journal club
0
11-17-2010 11:15 PM
[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'),...
nmrlearner
Journal club
0
08-22-2010 05:08 PM
[NMR paper] NMR studies of U1 snRNA recognition by the N-terminal RNP domain of the human U1A pro
NMR studies of U1 snRNA recognition by the N-terminal RNP domain of the human U1A protein.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR studies of U1 snRNA recognition by the N-terminal RNP domain of the human U1A protein.
EMBO J. 1994 Aug 15;13(16):3873-81
Authors: Howe PW, Nagai K, Neuhaus D, Varani G
The RNP domain is a very common motif found in hundreds of proteins, including many protein components of the RNA processing machinery. The 70-90...
nmrlearner
Journal club
0
08-22-2010 03:29 AM
[Nature network NMR forum] Journal club: structure of the ternary Prp31:15.5K:U4 snRNA complex (1 reply)
Journal club: structure of the ternary Prp31:15.5K:U4 snRNA complex (1 reply)
I would like to start the “journal club” section of the NMR forum by presenting my favorite paper from the recent literature.
The paper (in this weeks issue of Science) is, in my opinion at least, a perfect example of the ability of NMR to contribute to the structural analysis of a challenging RNA-protein complex
I chose this high-impact paper because the combination of biochemistry, NMR, and crystallography on a ternary complex is how I would like to tackle a challenging project that I am...
NMR structure of the 3' stem-loop from human U4 snRNA.
Linear Mode
