PDBsum entry 1y6t

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dna_rna metals links
3CO ×5
_NA ×2
Waters ×33
PDB id:
Name: RNA
Title: HIV-1 dis(mal) duplex co hexamine-soaked
Structure: 5'- r( Cp Up Up Gp Cp Up Gp Ap Gp Gp Up Gp Cp Ap Cp Ap Cp Ap Gp Cp Ap Ap G)-3'. Chain: a, b. Engineered: yes. Other_details: HIV-1 dis RNA
Source: Synthetic: yes
Biol. unit: Dimer (from PQS)
2.60Å     R-factor:   0.214     R-free:   0.255
Authors: E.Ennifar,P.Walter,P.Dumas
Key ref: E.Ennifar et al. (2003). A crystallographic study of the binding of 13 metal ions to two related RNA duplexes. Nucleic Acids Res, 31, 2671-2682. PubMed id: 12736317 DOI: 10.1093/nar/gkg350
07-Dec-04     Release date:   21-Dec-04    


DOI no: 10.1093/nar/gkg350 Nucleic Acids Res 31:2671-2682 (2003)
PubMed id: 12736317  
A crystallographic study of the binding of 13 metal ions to two related RNA duplexes.
E.Ennifar, P.Walter, P.Dumas.
Metal ions, and magnesium in particular, are known to be involved in RNA folding by stabilizing secondary and tertiary structures, and, as cofactors, in RNA enzymatic activity. We have conducted a systematic crystallographic analysis of cation binding to the duplex form of the HIV-1 RNA dimerization initiation site for the subtype-A and -B natural sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+, Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)6]3+ and [Ru (NH3)6]3+ were found to bind to the DIS duplex structure. Although the two sequences are very similar, strong differences were found in their cation binding properties. Divalent cations bind almost exclusively, as Mg2+, at 'Hoogsteen' sites of guanine residues, with a cation-dependent affinity for each site. Notably, a given cation can have very different affinities for a priori equivalent sites within the same molecule. Surprisingly, none of the two hexammines used were able to efficiently replace hexahydrated magnesium. Instead, [Co (NH3)4]3+ was seen bound by inner-sphere coordination to the RNA. This raises some questions about the practical use of [Co (NH3)6]3+ as a [Mg (H2O)6]2+ mimetic. Also very unexpected was the binding of the small Au3+ cation exactly between the Watson-Crick sites of a G-C base pair after an obligatory deprotonation of N1 of the guanine base. This extensive study of metal ion binding using X-ray crystallography significantly enriches our knowledge on the binding of middleweight or heavy metal ions to RNA, particularly compared with magnesium.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20460458 E.Ennifar, P.Walter, and P.Dumas (2010).
Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site.
  Nucleic Acids Res, 38, 5807-5816.
PDB codes: 2oiy 2oj0
20194520 J.Lipfert, A.Y.Sim, D.Herschlag, and S.Doniach (2010).
Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding.
  RNA, 16, 708-719.  
19703275 A.Y.Mulkidjanian, and M.Y.Galperin (2009).
On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
  Biol Direct, 4, 27.  
18560149 F.Pavelcik, and B.Schneider (2008).
Building of RNA and DNA double helices into electron density.
  Acta Crystallogr D Biol Crystallogr, 64, 620-626.  
18412127 J.Sarzyńska, K.Réblová, J.Sponer, and T.Kuliński (2008).
Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics.
  Biopolymers, 89, 732-746.  
18312410 J.Wrzesinski, and S.K.Jóźwiakowski (2008).
Structural basis for recognition of Co2+ by RNA aptamers.
  FEBS J, 275, 1651-1662.  
17637337 A.Y.Keel, R.P.Rambo, R.T.Batey, and J.S.Kieft (2007).
A general strategy to solve the phase problem in RNA crystallography.
  Structure, 15, 761-772.
PDB codes: 2pxb 2pxd 2pxe 2pxf 2pxk 2pxl 2pxp 2pxq 2pxt 2pxu 2pxv
17526525 D.Xu, T.Landon, N.L.Greenbaum, and M.O.Fenley (2007).
The electrostatic characteristics of G.U wobble base pairs.
  Nucleic Acids Res, 35, 3836-3847.  
17630326 E.Ennifar, S.Bernacchi, P.Wolff, and P.Dumas (2007).
Influence of C-5 halogenation of uridines on hairpin versus duplex RNA folding.
  RNA, 13, 1445-1452.  
17616553 K.J.Travers, N.Boyd, and D.Herschlag (2007).
Low specificity of metal ion binding in the metal ion core of a folded RNA.
  RNA, 13, 1205-1213.  
17720880 M.Forconi, J.A.Piccirilli, and D.Herschlag (2007).
Modulation of individual steps in group I intron catalysis by a peripheral metal ion.
  RNA, 13, 1656-1667.  
17131443 S.M.Dibrov, H.Johnston-Cox, Y.H.Weng, and T.Hermann (2007).
Functional architecture of HCV IRES domain II stabilized by divalent metal ions in the crystal and in solution.
  Angew Chem Int Ed Engl, 46, 226-229.
PDB code: 2nok
17940138 Y.Timsit, and S.Bombard (2007).
The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction.
  RNA, 13, 2098-2107.
PDB codes: 2r1s 2r20
16679451 E.Ennifar, J.C.Paillart, A.Bodlenner, P.Walter, J.M.Weibel, A.M.Aubertin, P.Pale, P.Dumas, and R.Marquet (2006).
Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell.
  Nucleic Acids Res, 34, 2328-2339.
PDB codes: 2fcx 2fcy 2fcz 2fd0
16698544 F.Rázga, M.Zacharias, K.Réblová, J.Koca, and J.Sponer (2006).
RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics.
  Structure, 14, 825-835.  
16538608 K.Réblová, F.Lankas, F.Rázga, M.V.Krasovska, J.Koca, and J.Sponer (2006).
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations.
  Biopolymers, 82, 504-520.  
16510980 R.Utsunomiya, K.Suto, D.Balasundaresan, A.Fukamizu, P.K.Kumar, and H.Mizuno (2006).
Structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G.U base pairs.
  Acta Crystallogr D Biol Crystallogr, 62, 331-338.
PDB code: 2ao5
16269545 B.H.Mooers, J.S.Logue, and J.A.Berglund (2005).
The structural basis of myotonic dystrophy from the crystal structure of CUG repeats.
  Proc Natl Acad Sci U S A, 102, 16626-16631.
PDB code: 1zev
15869389 D.E.Draper, D.Grilley, and A.M.Soto (2005).
Ions and RNA folding.
  Annu Rev Biophys Biomol Struct, 34, 221-243.  
16430131 P.Guo (2005).
RNA nanotechnology: engineering, assembly and applications in detection, gene delivery and therapy.
  J Nanosci Nanotechnol, 5, 1964-1982.  
15846405 Y.Tanaka, and K.Taira (2005).
Detection of RNA nucleobase metalation by NMR spectroscopy.
  Chem Commun (Camb), (), 2069-2079.  
15339800 K.Réblová, N.Spacková, J.Koca, N.B.Leontis, and J.Sponer (2004).
Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.
  Biophys J, 87, 3397-3412.  
15556400 M.Egli (2004).
Nucleic acid crystallography: current progress.
  Curr Opin Chem Biol, 8, 580-591.  
15298889 M.Rueda, E.Cubero, C.A.Laughton, and M.Orozco (2004).
Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?
  Biophys J, 87, 800-811.  
14627827 K.Réblová, N.Spacková, J.E.Sponer, J.Koca, and J.Sponer (2003).
Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets.
  Nucleic Acids Res, 31, 6942-6952.  
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.