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PDBsum entry 1a60
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RNA PDB id
1a60

 

 

 

 

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Contents
DNA/RNA
PDB id:
1a60
Name: RNA
Title: Nmr structure of a classical pseudoknot: interplay of single-and double-stranded RNA, 24 structures
Structure: Tymv pseudoknot. Chain: a. Fragment: acceptor arm of tymv tRNA-like structure
Source: Turnip yellow mosaic virus. Organism_taxid: 12154
NMR struc: 24 models
Authors: M.H.Kolk,M.Van Der Graaf,S.S.Wijmenga,C.W.A.Pleij,H.A.Heus, C.W.Hilbers
Key ref:
M.H.Kolk et al. (1998). NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA. Science, 280, 434-438. PubMed id: 9545221 DOI: 10.1126/science.280.5362.434
Date:
04-Mar-98     Release date:   27-May-98    
 Headers
 References

DNA/RNA chain
  G-G-G-A-G-C-U-C-A-A-C-U-C-U-C-C-C-C-C-C-C-U-U-U-U-C-C-G-A-G-G-G-U-C-A-U-C-G-G- 44 bases

 

 
DOI no: 10.1126/science.280.5362.434 Science 280:434-438 (1998)
PubMed id: 9545221  
 
 
NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA.
M.H.Kolk, M.van der Graaf, S.S.Wijmenga, C.W.Pleij, H.A.Heus, C.W.Hilbers.
 
  ABSTRACT  
 
Pseudoknot formation folds the 3' ends of many plant viral genomic RNAs into structures that resemble transfer RNA in global folding and in their reactivity to transfer RNA-specific proteins. The solution structure of the pseudoknotted T arm and acceptor arm of the transfer RNA-like structure of turnip yellow mosaic virus (TYMV) was determined by nuclear magnetic resonance (NMR) spectroscopy. The molecule is stabilized by the hairpin formed by the 5' end of the RNA, and by the intricate interactions related to the loops of the pseudoknot. Loop 1 spans the major groove of the helix with only two of its four nucleotides. Loop 2, which crosses the minor groove, interacts closely with its opposing helix, in particular through hydrogen bonds with a highly conserved adenine. The structure resulting from this interaction between the minor groove and single-stranded RNA at helical junctions displays internal mobility, which may be a general feature of RNA pseudoknots that regulates their interaction with proteins or other RNA molecules.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Detail of the structure showing the hydrogen bonds found between loop 2 and stem 1 (see text). The highly DEPC-reactive N-7^ atom of A35 is highlighted in yellow. 		Figure 4.
Fig. 4. View into the major groove of stem 2 showing the distinct turn in loop 1. The coloring scheme is identical to that of Fig. 2. U24 and U23 are not involved in base-pairing interactions with the opposite bases of A41 and C42. Nucleotides C21 and U22, spanning the major groove, are drawn in thin lines. The curved arrow denotes the direction of the RNA chain.
 
  The above figures are reprinted by permission from the AAAs: Science (1998, 280, 434-438) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20495679 B.Liu, D.H.Mathews, and D.H.Turner (2010).
RNA pseudoknots: folding and finding.
  F1000 Biol Rep, 2, 0.  
18621088 D.P.Giedroc, and P.V.Cornish (2009).
Frameshifting RNA pseudoknots: structure and mechanism.
  Virus Res, 139, 193-208.
PDB codes: 2rp0 2rp1
  20461158 Dhar, S.Ganguli, and A.Datta (2009).
Targeting pseudoknots in H5N1 hemagglutinin using designed aptamers.
  Bioinformation, 4, 193-196.  
19397915 E.Kierzek, S.M.Christensen, T.H.Eickbush, R.Kierzek, D.H.Turner, and W.N.Moss (2009).
Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints.
  J Mol Biol, 390, 428-442.  
19144910 J.A.Hammond, R.P.Rambo, M.E.Filbin, and J.S.Kieft (2009).
Comparison and functional implications of the 3D architectures of viral tRNA-like structures.
  RNA, 15, 294-307.  
18456842 F.Ding, S.Sharma, P.Chalasani, V.V.Demidov, N.E.Broude, and N.V.Dokholyan (2008).
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.
  RNA, 14, 1164-1173.  
18281388 S.Fulle, and H.Gohlke (2008).
Analyzing the flexibility of RNA structures by constraint counting.
  Biophys J, 94, 4202-4219.  
17401565 X.Wang, G.Kapral, L.Murray, D.Richardson, J.Richardson, and J.Snoeyink (2008).
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.
  J Math Biol, 56, 253-278.  
17381343 B.Rastegari, and A.Condon (2007).
Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications.
  J Comput Biol, 14, 16-32.  
17632571 I.Brierley, S.Pennell, and R.J.Gilbert (2007).
Viral RNA pseudoknots: versatile motifs in gene expression and replication.
  Nat Rev Microbiol, 5, 598-610.  
17581985 N.Beerens, and E.J.Snijder (2007).
An RNA pseudoknot in the 3' end of the arterivirus genome has a critical role in regulating viral RNA synthesis.
  J Virol, 81, 9426-9436.  
17878940 W.K.Dawson, K.Fujiwara, and G.Kawai (2007).
Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding.
  PLoS ONE, 2, e905.  
16865417 P.V.Cornish, D.P.Giedroc, and M.Hennig (2006).
Dissecting non-canonical interactions in frameshift-stimulating mRNA pseudoknots.
  J Biomol NMR, 35, 209-223.  
16709732 S.Cao, and S.J.Chen (2006).
Predicting RNA pseudoknot folding thermodynamics.
  Nucleic Acids Res, 34, 2634-2652.  
16595798 S.Nonin-Lecomte, B.Felden, and F.Dardel (2006).
NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation.
  Nucleic Acids Res, 34, 1847-1853.
PDB code: 2g1w
15994188 C.H.Huang, C.L.Lu, and H.T.Chiu (2005).
A heuristic approach for detecting RNA H-type pseudoknots.
  Bioinformatics, 21, 3501-3508.  
15155850 R.H.Guenther, T.L.Sit, H.S.Gracz, M.A.Dolan, H.L.Townsend, G.Liu, W.H.Newman, P.F.Agris, and S.A.Lommel (2004).
Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus.
  Nucleic Acids Res, 32, 2819-2828.  
14745440 R.K.Sigel, D.G.Sashital, D.L.Abramovitz, A.G.Palmer, S.E.Butcher, and A.M.Pyle (2004).
Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.
  Nat Struct Mol Biol, 11, 187-192.
PDB code: 1r2p
12525617 C.T.Ranjith-Kumar, X.Zhang, and C.C.Kao (2003).
Enhancer-like activity of a brome mosaic virus RNA promoter.
  J Virol, 77, 1830-1839.  
12364602 M.H.de Smit, A.P.Gultyaev, M.Hilge, H.H.Bink, S.Barends, B.Kraal, and C.W.Pleij (2002).
Structural variation and functional importance of a D-loop-T-loop interaction in valine-accepting tRNA-like structures of plant viral RNAs.
  Nucleic Acids Res, 30, 4232-4240.  
12762025 I.Brierley, and S.Pennell (2001).
Structure and function of the stimulatory RNAs involved in programmed eukaryotic-1 ribosomal frameshifting.
  Cold Spring Harb Symp Quant Biol, 66, 233-248.  
10590114 B.A.Deiman, P.W.Verlaan, and C.W.Pleij (2000).
In vitro transcription by the turnip yellow mosaic virus RNA polymerase: a comparison with the alfalfa mosaic virus and brome mosaic virus replicases.
  J Virol, 74, 264-271.  
10821696 J.Wientges, J.Pütz, R.Giegé, C.Florentz, and A.Schwienhorst (2000).
Selection of viral RNA-derived tRNA-like structures with improved valylation activities.
  Biochemistry, 39, 6207-6218.  
11142381 P.J.Michiels, C.H.Schouten, C.W.Hilbers, and H.A.Heus (2000).
Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site.
  RNA, 6, 1821-1832.
PDB code: 1e4p
10786851 T.Dale, R.Smith, and M.J.Serra (2000).
A test of the model to predict unusually stable RNA hairpin loop stability.
  RNA, 6, 608-615.  
11142379 V.G.Kolupaeva, T.V.Pestova, and C.U.Hellen (2000).
Ribosomal binding to the internal ribosomal entry site of classical swine fever virus.
  RNA, 6, 1791-1807.  
10917594 W.J.Melchers, J.M.Bakkers, H.J.Bruins Slot, J.M.Galama, V.I.Agol, and E.V.Pilipenko (2000).
Cross-talk between orientation-dependent recognition determinants of a complex control RNA element, the enterovirus oriR.
  RNA, 6, 976-987.  
10410795 A.R.Ferré-D'Amaré, and J.A.Doudna (1999).
RNA folds: insights from recent crystal structures.
  Annu Rev Biophys Biomol Struct, 28, 57-73.  
10359761 D.Gilley, and E.H.Blackburn (1999).
The telomerase RNA pseudoknot is critical for the stable assembly of a catalytically active ribonucleoprotein.
  Proc Natl Acad Sci U S A, 96, 6621-6625.  
10647177 F.Jiang, A.Gorin, W.Hu, A.Majumdar, S.Baskerville, W.Xu, A.Ellington, and D.J.Patel (1999).
Anchoring an extended HTLV-1 Rex peptide within an RNA major groove containing junctional base triples.
  Structure, 7, 1461-1472.
PDB codes: 1c4j 1exy
10024177 J.A.Holland, M.R.Hansen, Z.Du, and D.W.Hoffman (1999).
An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2.
  RNA, 5, 257-271.
PDB code: 2tpk
10469663 R.C.Olsthoorn, S.Mertens, F.T.Brederode, and J.F.Bol (1999).
A conformational switch at the 3' end of a plant virus RNA regulates viral replication.
  EMBO J, 18, 4856-4864.  
11701820 T.W.Dreher (1999).
FUNCTIONS OF THE 3'-UNTRANSLATED REGIONS OF POSITIVE STRAND RNA VIRAL GENOMES.
  Annu Rev Phytopathol, 37, 151-174.  
9724720 B.Felden, and R.Giegé (1998).
Resected RNA pseudoknots and their recognition by histidyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 95, 10431-10436.  
9818148 C.H.Lin, W.Wang, R.A.Jones, and D.J.Patel (1998).
Formation of an amino-acid-binding pocket through adaptive zippering-up of a large DNA hairpin loop.
  Chem Biol, 5, 555-572.
PDB code: 2arg
10333742 C.W.Hilbers, P.J.Michiels, and H.A.Heus (1998).
New developments in structure determination of pseudoknots.
  Biopolymers, 48, 137-153.  
10333740 D.J.Patel (1998).
Molecular insights into the RNA world.
  Biopolymers, 48, 97.  
9705510 H.F.Becker, Y.Motorin, C.Florentz, R.Giegé, and H.Grosjean (1998).
Pseudouridine and ribothymidine formation in the tRNA-like domain of turnip yellow mosaic virus RNA.
  Nucleic Acids Res, 26, 3991-3997.  
9857204 M.H.Kolk, M.van der Graaf, C.T.Fransen, S.S.Wijmenga, C.W.Pleij, H.A.Heus, and C.W.Hilbers (1998).
Structure of the 3'-hairpin of the TYMV pseudoknot: preformation in RNA folding.
  EMBO J, 17, 7498-7504.
PDB code: 3php
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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