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PDBsum entry 373d
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Ribonucleic acid PDB id
373d

 

 

 

 

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Contents
DNA/RNA
Waters ×49
Superseded by: 413d
PDB id:
373d
Name: Ribonucleic acid
Title: A'-RNA conformation in the crystal structure of r(ugagcuucggcuc)
Structure: RNA (5'-r( Up Gp Ap Gp Cp Up Up Cp Gp Gp Cp Up C)-3'). Chain: a. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PDB file)
Resolution:
1.80Å     R-factor:   0.167    
Authors: Y.Tanaka,K.-I.Tomita,T.Sakata,H.Hiroaki,T.Tanaka,S.Uesugi, Y.Kyogoku,S.Fujii
Key ref:
C.C.Correll et al. (1997). Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell, 91, 705-712. PubMed id: 9393863 DOI: 10.1016/S0092-8674(00)80457-2
Date:
13-Jan-98     Release date:   25-Feb-98    
 Headers
 References

DNA/RNA chain
  U-G-A-G-C-U-U-C-G-G-C-U-C 13 bases

 

 
DOI no: 10.1016/S0092-8674(00)80457-2 Cell 91:705-712 (1997)
PubMed id: 9393863  
 
 
Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.
C.C.Correll, B.Freeborn, P.B.Moore, T.A.Steitz.
 
  ABSTRACT  
 
Two new RNA structures portray how non-Watson-Crick base pairs and metal ions can produce a unique RNA shape suitable for recognition by proteins. The crystal structures of a 62 nt domain of E. coli 5S ribosomal RNA and a duplex dodecamer encompassing an internal loop E have been determined at 3.0 and 1.5 A, respectively. This loop E region is distorted by three "cross-strand purine stacks" and three novel, water-mediated noncanonical base pairs and stabilized by a four metal ion zipper. These features give its minor groove a unique hydrogen-bonding surface and make the adjacent major groove wide enough to permit recognition by the ribosomal protein L25, which is expected to bind to this surface.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The Cross-Strand Purine Stack(A) A cross-strand A stack showing A104 from one strand in blue stacked on A73 of the other strand in yellow. The position of the kink at the β and γ angles of the yellow backbone is indicated.(B) Nucleotide sequences of the six observed cross-strand A stacks ([42, 32, 39 and 11]) and the consensus for bulged and nonbulged A stacks. 		Figure 5.
Figure 5. Stereo Diagrams of Metal Sites A through E(A) A frequently observed G•G metal ion binding site showing the involvement of water in outer-sphere coordination.(B) The “metal ion zipper” in the narrow major groove of loop E. The two strands are in green and blue.
 
  The above figures are reprinted by permission from Cell Press: Cell (1997, 91, 705-712) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22678284 A.Ren, K.R.Rajashankar, and D.J.Patel (2012).
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  Nature, 486, 85-89.
PDB codes: 3vrs 4en5 4ena 4enb 4enc
21333656 J.Wang, and E.P.Nikonowicz (2011).
Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA.
  J Mol Biol, 408, 99.  
20554048 A.R.Ferré-D'Amaré (2010).
Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.
  Methods, 52, 159-167.  
20696653 C.Zhong, H.Tang, and S.Zhang (2010).
RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.
  Nucleic Acids Res, 38, e176.  
20110252 J.Wang, T.M.Henkin, and E.P.Nikonowicz (2010).
NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA.
  Nucleic Acids Res, 38, 3388-3398.
PDB code: 2khy
20230868 P.Guo, O.Coban, N.M.Snead, J.Trebley, S.Hoeprich, S.Guo, and Y.Shu (2010).
Engineering RNA for targeted siRNA delivery and medical application.
  Adv Drug Deliv Rev, 62, 650-666.  
20473315 S.L.Bullock, I.Ringel, D.Ish-Horowicz, and P.J.Lukavsky (2010).
A'-form RNA helices are required for cytoplasmic mRNA transport in Drosophila.
  Nat Struct Mol Biol, 17, 703-709.
PDB codes: 2ke6 2kur 2kuu 2kuv 2kuw
20223772 X.J.Lu, W.K.Olson, and H.J.Bussemaker (2010).
The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.
  Nucleic Acids Res, 38, 4868-4876.  
19298181 A.Roth, and R.R.Breaker (2009).
The structural and functional diversity of metabolite-binding riboswitches.
  Annu Rev Biochem, 78, 305-334.  
19528080 C.L.Zirbel, J.E.Sponer, J.Sponer, J.Stombaugh, and N.B.Leontis (2009).
Classification and energetics of the base-phosphate interactions in RNA.
  Nucleic Acids Res, 37, 4898-4918.  
18638512 P.J.Lukavsky (2009).
Structure and function of HCV IRES domains.
  Virus Res, 139, 166-171.  
18784651 A.Serganov, L.Huang, and D.J.Patel (2008).
Structural insights into amino acid binding and gene control by a lysine riboswitch.
  Nature, 455, 1263-1267.
PDB codes: 3dig 3dil 3dim 3dio 3diq 3dir 3dis 3dix 3diy 3diz 3dj0 3dj2
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  Nucleic Acids Res, 36, 970-983.  
18952821 I.Carter-O'Connell, D.Booth, B.Eason, and N.Grover (2008).
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  RNA, 14, 2550-2556.  
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  Biophys J, 95, 3892-3905.  
18192612 J.S.Richardson, B.Schneider, L.W.Murray, G.J.Kapral, R.M.Immormino, J.J.Headd, D.C.Richardson, D.Ham, E.Hershkovits, L.D.Williams, K.S.Keating, A.M.Pyle, D.Micallef, J.Westbrook, and H.M.Berman (2008).
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
  RNA, 14, 465-481.  
18441048 O.Fedorova, and A.M.Pyle (2008).
A conserved element that stabilizes the group II intron active site.
  RNA, 14, 1048-1056.  
18772248 P.S.Pallan, C.Kreutz, S.Bosio, R.Micura, and M.Egli (2008).
Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m2 2G:A pairs.
  RNA, 14, 2125-2135.
PDB code: 3cjz
17981525 R.Russell (2008).
RNA misfolding and the action of chaperones.
  Front Biosci, 13, 1.  
18435545 Y.Lin, and C.L.Kielkopf (2008).
X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines.
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PDB codes: 3cgp 3cgq 3cgr 3cgs
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The electrostatic characteristics of G.U wobble base pairs.
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Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine.
  Nucleic Acids Res, 35, 5108-5119.  
17200997 M.C.Erat, O.Zerbe, T.Fox, and R.K.Sigel (2007).
Solution structure of domain 6 from a self-splicing group II intron ribozyme: a Mg(2+) binding site is located close to the stacked branch adenosine.
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PDB code: 2aht
17612557 M.R.Stahley, P.L.Adams, J.Wang, and S.A.Strobel (2007).
Structural metals in the group I intron: a ribozyme with a multiple metal ion core.
  J Mol Biol, 372, 89.  
17438124 R.A.Owens, and T.Baumstark (2007).
Structural differences within the loop E motif imply alternative mechanisms of viroid processing.
  RNA, 13, 824-834.  
17080418 S.E.McDowell, N.Spacková, J.Sponer, and N.G.Walter (2007).
Molecular dynamics simulations of RNA: an in silico single molecule approach.
  Biopolymers, 85, 169-184.  
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The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction.
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Acid-base properties of the nucleic-acid model 2'-deoxyguanylyl(5'-->3')-2'-deoxy-5'-guanylate, d(pGpG)3-, and of related guanine derivatives.
  Org Biomol Chem, 4, 1085-1090.  
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  Nucleic Acids Res, 34, W405-W411.  
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  Nucleic Acids Res, 34, D131-D134.  
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  Annu Rev Biophys Biomol Struct, 34, 221-243.  
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  RNA, 11, 1688-1700.  
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RNA nanotechnology: engineering, assembly and applications in detection, gene delivery and therapy.
  J Nanosci Nanotechnol, 5, 1964-1982.  
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Secondary structure, high variability and conserved motifs for domain III of 12S rRNA in the Arthropleona (Hexapoda; Collembola).
  Insect Mol Biol, 13, 659-670.  
  21171616 D.Shu, W.D.Moll, Z.Deng, C.Mao, and P.Guo (2004).
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  Nano Lett, 4, 1717-1723.  
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  J Mol Model, 10, 408-417.  
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  Biophys J, 87, 3397-3412.  
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  Biopolymers, 73, 151-161.  
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Anion binding to nucleic acids.
  Structure, 12, 379-388.  
15103128 S.B.Jang, K.Baeyens, M.S.Jeong, J.SantaLucia, D.Turner, and S.R.Holbrook (2004).
Structures of two RNA octamers containing tandem G.A base pairs.
  Acta Crystallogr D Biol Crystallogr, 60, 829-835.
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The kink-turn motif in RNA is dimorphic, and metal ion-dependent.
  RNA, 10, 254-264.  
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Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution.
  Structure, 12, 893-903.
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The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure.
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Solution structures of stem-loop RNAs that bind to the two N-terminal RNA-binding domains of nucleolin.
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Analysis of RNA motifs.
  Curr Opin Struct Biol, 13, 300-308.  
14561883 O.Fernández-Miragall, and E.Martínez-Salas (2003).
Structural organization of a viral IRES depends on the integrity of the GNRA motif.
  RNA, 9, 1333-1344.  
12560495 O.Schrader, T.Baumstark, and D.Riesner (2003).
A mini-RNA containing the tetraloop, wobble-pair and loop E motifs of the central conserved region of potato spindle tuber viroid is processed into a minicircle.
  Nucleic Acids Res, 31, 988-998.  
12837388 P.Auffinger, L.Bielecki, and E.Westhof (2003).
The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations.
  Chem Biol, 10, 551-561.  
12549908 S.I.Chamberlin, and K.M.Weeks (2003).
Differential helix stabilities and sites pre-organized for tertiary interactions revealed by monitoring local nucleotide flexibility in the bI5 group I intron RNA.
  Biochemistry, 42, 901-909.  
12554875 S.Szép, J.Wang, and P.B.Moore (2003).
The crystal structure of a 26-nucleotide RNA containing a hook-turn.
  RNA, 9, 44-51.
PDB code: 1mhk
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Crystal structures of r(GGUCACAGCCC)2.
  Acta Crystallogr D Biol Crystallogr, 59, 423-432.
PDB codes: 1kd3 1kd4 1kd5
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  EMBO J, 21, 5281-5291.  
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Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA.
  EMBO J, 21, 2253-2262.  
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Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules.
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The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs.
  BMC Bioinformatics, 3, 2.  
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Effects of magnesium ions on the stabilization of RNA oligomers of defined structures.
  RNA, 8, 307-323.  
12364603 M.Olejniczak, Z.Gdaniec, A.Fischer, T.Grabarkiewicz, L.Bielecki, and R.W.Adamiak (2002).
The bulge region of HIV-1 TAR RNA binds metal ions in solution.
  Nucleic Acids Res, 30, 4241-4249.  
  18629252 N.B.Leontis, and E.Westhof (2002).
The annotation of RNA motifs.
  Comp Funct Genomics, 3, 518-524.  
12177293 N.B.Leontis, J.Stombaugh, and E.Westhof (2002).
The non-Watson-Crick base pairs and their associated isostericity matrices.
  Nucleic Acids Res, 30, 3497-3531.  
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Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair.
  RNA, 8, 659-670.  
12364604 S.Lemieux, and F.Major (2002).
RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire.
  Nucleic Acids Res, 30, 4250-4263.  
12166647 S.Lima, J.Hildenbrand, A.Korostelev, S.Hattman, and H.Li (2002).
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  RNA, 8, 924-932.
PDB code: 1kfo
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Structure of the SRP19 RNA complex and implications for signal recognition particle assembly.
  Nature, 417, 767-771.
PDB code: 1lng
12358430 U.Nagaswamy, and G.E.Fox (2002).
Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs.
  RNA, 8, 1112-1119.  
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The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove.
  Nucleic Acids Res, 29, 4144-4153.
PDB code: 1i7j
  11333226 F.Pâques, G.F.Richard, and J.E.Haber (2001).
Expansions and contractions in 36-bp minisatellites by gene conversion in yeast.
  Genetics, 158, 155-166.  
11891627 J.Sühnel (2001).
Beyond nucleic acid base pairs: from triads to heptads.
  Biopolymers, 61, 32-51.  
11286889 K.Juneau, E.Podell, D.J.Harrington, and T.R.Cech (2001).
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions.
  Structure, 9, 221-231.
PDB code: 1hr2
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Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair.
  Biochemistry, 40, 2478-2483.  
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Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 219-224.
PDB code: 439d
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Geometric nomenclature and classification of RNA base pairs.
  RNA, 7, 499-512.  
11296253 P.Nissen, J.A.Ippolito, N.Ban, P.B.Moore, and T.A.Steitz (2001).
RNA tertiary interactions in the large ribosomal subunit: the A-minor motif.
  Proc Natl Acad Sci U S A, 98, 4899-4903.  
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PDB code: 1feu
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Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.
  RNA, 7, 692-701.
PDB code: 1iq4
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Proximity of the invariant loop of U5 snRNA to the second intron residue during pre-mRNA splicing.
  EMBO J, 20, 3577-3586.  
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Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments.
  Nucleic Acids Res, 29, 1208-1215.
PDB codes: 1i0f 1i0g 1i0j 1i0k 1i0m 1i0n 1i0o 1i0p 1i0q 1i0t
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On the wobble GoU and related pairs.
  RNA, 6, 9.  
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A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome.
  Structure, 8, 937-948.  
10903943 D.Sussman, and C.Wilson (2000).
A water channel in the core of the vitamin B(12) RNA aptamer.
  Structure, 8, 719-727.
PDB code: 1et4
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Helix P4 is a divalent metal ion binding site in the conserved core of the ribonuclease P ribozyme.
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RNA folding: beyond Watson-Crick pairs.
  Structure, 8, R55-R65.  
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Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.
  Nucleic Acids Res, 28, 1760-1766.
PDB codes: 1dno 1dnt 1dnx 1dnz
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The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited.
  RNA, 6, 1091-1105.
PDB code: 1ehz
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Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
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Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.
  Structure, 8, 527-540.
PDB code: 1duh
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The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability.
  Proc Natl Acad Sci U S A, 97, 5107-5112.
PDB code: 1duq
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NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs.
  Biochemistry, 39, 11748-11762.
PDB codes: 1f5g 1f5h
10696113 M.Lu, and T.A.Steitz (2000).
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
  Proc Natl Acad Sci U S A, 97, 2023-2028.
PDB code: 1dfu
10592212 M.Szymanski, M.Z.Barciszewska, J.Barciszewski, and V.A.Erdmann (2000).
5S ribosomal RNA database Y2K.
  Nucleic Acids Res, 28, 166-167.  
10937989 N.Ban, P.Nissen, J.Hansen, P.B.Moore, and T.A.Steitz (2000).
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
  Science, 289, 905-920.
PDB code: 1ffk
10694382 S.E.Butcher, F.H.Allain, and J.Feigon (2000).
Determination of metal ion binding sites within the hairpin ribozyme domains by NMR.
  Biochemistry, 39, 2174-2182.  
10924119 S.J.Schroeder, and D.H.Turner (2000).
Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA.
  Biochemistry, 39, 9257-9274.  
10739932 S.Lorenz, M.Perbandt, C.Lippmann, K.Moore, L.J.DeLucas, C.Betzel, and V.A.Erdmann (2000).
Crystallization of engineered Thermus flavus 5S rRNA under earth and microgravity conditions.
  Acta Crystallogr D Biol Crystallogr, 56, 498-500.  
10864040 S.O.Shan, and D.Herschlag (2000).
An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction.
  RNA, 6, 795-813.  
11058117 T.C.Kuo, and D.L.Herrin (2000).
Quantitative studies of Mn(2+)-promoted specific and non-specific cleavages of a large RNA: Mn(2+)-GAAA ribozymes and the evolution of small ribozymes.
  Nucleic Acids Res, 28, 4197-4206.  
10999608 Y.Xiong, and M.Sundaralingam (2000).
Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge.
  RNA, 6, 1316-1324.
PDB codes: 1dqf 1dqh
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.  
10052954 B.Pan, S.N.Mitra, and M.Sundaralingam (1999).
Crystal structure of an RNA 16-mer duplex R(GCAGAGUUAAAUCUGC)2 with nonadjacent G(syn).A+(anti) mispairs.
  Biochemistry, 38, 2826-2831.
PDB code: 420d
10397790 C.Schneider, and J.Sühnel (1999).
A molecular dynamics simulation of the flavin mononucleotide-RNA aptamer complex.
  Biopolymers, 50, 287-302.  
10074350 E.A.Doherty, D.Herschlag, and J.A.Doudna (1999).
Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme.
  Biochemistry, 38, 2982-2990.  
10574792 E.Ennifar, M.Yusupov, P.Walter, R.Marquet, B.Ehresmann, C.Ehresmann, and P.Dumas (1999).
The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges.
  Structure, 7, 1439-1449.
PDB codes: 1y99 462d
10497122 J.H.Cate, M.M.Yusupov, G.Z.Yusupova, T.N.Earnest, and H.F.Noller (1999).
X-ray crystal structures of 70S ribosome functional complexes.
  Science, 285, 2095-2104.
PDB code: 486d
9876123 J.P.Rife, S.C.Stallings, C.C.Correll, A.Dallas, T.A.Steitz, and P.B.Moore (1999).
Comparison of the crystal and solution structures of two RNA oligonucleotides.
  Biophys J, 76, 65-75.  
10339556 J.Pan, D.Thirumalai, and S.A.Woodson (1999).
Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics.
  Proc Natl Acad Sci U S A, 96, 6149-6154.  
10454606 J.Wöhnert, A.J.Dingley, M.Stoldt, M.Görlach, S.Grzesiek, and L.R.Brown (1999).
Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy.
  Nucleic Acids Res, 27, 3104-3110.  
10574798 K.Wild, O.Weichenrieder, G.A.Leonard, and S.Cusack (1999).
The 2 A structure of helix 6 of the human signal recognition particle RNA.
  Structure, 7, 1345-1352.
PDB code: 1d4r
10573119 M.B.Elliott, P.A.Gottlieb, and P.Gollnick (1999).
Probing the TRAP-RNA interaction with nucleoside analogs.
  RNA, 5, 1277-1289.  
10562563 M.Stoldt, J.Wöhnert, O.Ohlenschläger, M.Görlach, and L.R.Brown (1999).
The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.
  EMBO J, 18, 6508-6521.
PDB code: 1d6k
9876122 P.Auffinger, S.Louise-May, and E.Westhof (1999).
Molecular dynamics simulations of solvated yeast tRNA(Asp).
  Biophys J, 76, 50-64.  
10872451 P.B.Moore (1999).
Structural motifs in RNA.
  Annu Rev Biochem, 68, 287-300.  
10580471 P.Babin, M.Dolan, P.Wollenzien, and R.R.Gutell (1999).
Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling.
  RNA, 5, 1430-1439.  
10737860 P.J.Beuning, and K.Musier-Forsyth (1999).
Transfer RNA recognition by aminoacyl-tRNA synthetases.
  Biopolymers, 52, 1.  
10368282 P.Nissen, S.Thirup, M.Kjeldgaard, and J.Nyborg (1999).
The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA.
  Structure, 7, 143-156.
PDB code: 1b23
10555960 P.S.Klosterman, S.A.Shah, and T.A.Steitz (1999).
Crystal structures of two plasmid copy control related RNA duplexes: An 18 base pair duplex at 1.20 A resolution and a 19 base pair duplex at 1.55 A resolution.
  Biochemistry, 38, 14784-14792.
PDB codes: 1qc0 1qcu
10322215 R.K.Agrawal, and J.Frank (1999).
Structural studies of the translational apparatus.
  Curr Opin Struct Biol, 9, 215-221.  
10400475 S.Cusack (1999).
RNA-protein complexes.
  Curr Opin Struct Biol, 9, 66-73.  
10600106 Y.G.Gao, H.Robinson, R.Sanishvili, A.Joachimiak, and A.H.Wang (1999).
Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution.
  Biochemistry, 38, 16452-16460.
PDB codes: 1d8x 1d9r 1dcr
9814765 A.Montpetit, C.Payant, J.M.Nolan, and L.Brakier-Gingras (1998).
Analysis of the conformation of the 3' major domain of Escherichia coli16S ribosomal RNA using site-directed photoaffinity crosslinking.
  RNA, 4, 1455-1466.  
9841391 B.L.Golden, A.R.Gooding, E.R.Podell, and T.R.Cech (1998).
A preorganized active site in the crystal structure of the Tetrahymena ribozyme.
  Science, 282, 259-264.
PDB code: 1grz
9545425 C.Berens, B.Streicher, R.Schroeder, and W.Hillen (1998).
Visualizing metal-ion-binding sites in group I introns by iron(II)-mediated Fenton reactions.
  Chem Biol, 5, 163-175.  
9811818 C.C.Correll, A.Munishkin, Y.L.Chan, Z.Ren, I.G.Wool, and T.A.Steitz (1998).
Crystal structure of the ribosomal RNA domain essential for binding elongation factors.
  Proc Natl Acad Sci U S A, 95, 13436-13441.
PDB code: 430d
9699612 C.M.Ogata (1998).
MAD phasing grows up.
  Nat Struct Biol, 5, 638-640.  
9564052 C.Mayer-Jung, D.Moras, and Y.Timsit (1998).
Hydration and recognition of methylated CpG steps in DNA.
  EMBO J, 17, 2709-2718.
PDB codes: 382d 383d 384d
10333740 D.J.Patel (1998).
Molecular insights into the RNA world.
  Biopolymers, 48, 97.  
9666322 G.L.Conn, and D.E.Draper (1998).
RNA structure.
  Curr Opin Struct Biol, 8, 278-285.  
9707559 J.A.Ippolito, and T.A.Steitz (1998).
A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation.
  Proc Natl Acad Sci U S A, 95, 9819-9824.
PDB code: 397d
9671051 J.Kufel, and L.A.Kirsebom (1998).
The P15-loop of Escherichia coli RNase P RNA is an autonomous divalent metal ion binding domain.
  RNA, 4, 777-788.  
9769095 K.Seggerson, and P.B.Moore (1998).
Structure and stability of variants of the sarcin-ricin loop of 28S rRNA: NMR studies of the prokaryotic SRL and a functional mutant.
  RNA, 4, 1203-1215.  
9731769 L.Jiang, and D.J.Patel (1998).
Solution structure of the tobramycin-RNA aptamer complex.
  Nat Struct Biol, 5, 769-774.
PDB code: 2tob
9799245 M.Stoldt, J.Wöhnert, M.Görlach, and L.R.Brown (1998).
The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases.
  EMBO J, 17, 6377-6384.
PDB code: 1b75
9740131 N.B.Leontis, and E.Westhof (1998).
The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.
  RNA, 4, 1134-1153.  
9657144 N.Ban, B.Freeborn, P.Nissen, P.Penczek, R.A.Grassucci, R.Sweet, J.Frank, P.B.Moore, and T.A.Steitz (1998).
A 9 A resolution X-ray crystallographic map of the large ribosomal subunit.
  Cell, 93, 1105-1115.  
9769102 N.Polacek, and A.Barta (1998).
Metal ion probing of rRNAs: evidence for evolutionarily conserved divalent cation binding pockets.
  RNA, 4, 1282-1294.  
9485366 P.Zheng, C.J.Burrows, and S.E.Rokita (1998).
Nickel- and cobalt-dependent reagents identify structural features of RNA that are not detected by dimethyl sulfate or RNase T1.
  Biochemistry, 37, 2207-2214.  
9666324 S.A.Woodson, and N.B.Leontis (1998).
Structure and dynamics of ribosomal RNA.
  Curr Opin Struct Biol, 8, 294-300.  
9765233 S.Xirasagar, M.B.Elliott, W.Bartolini, P.Gollnick, and P.A.Gottlieb (1998).
RNA structure inhibits the TRAP (trp RNA-binding attenuation protein)-RNA interaction.
  J Biol Chem, 273, 27146-27153.  
9922178 T.E.Horton, D.R.Clardy, and V.J.DeRose (1998).
Electron paramagnetic resonance spectroscopic measurement of Mn2+ binding affinities to the hammerhead ribozyme and correlation with cleavage activity.
  Biochemistry, 37, 18094-18101.  
9782053 T.Hermann, and E.Westhof (1998).
Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations.
  Structure, 6, 1303-1314.  
10333741 V.K.Misra, and D.E.Draper (1998).
On the role of magnesium ions in RNA stability.
  Biopolymers, 48, 113-135.  
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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