spacer
spacer

PDBsum entry 1j8g

Go to PDB code: 
dna_rna ligands metals links
RNA PDB id
1j8g
Jmol
Contents
DNA/RNA
Ligands
SPM
Metals
_NA ×2
_CA ×3
_SR ×8
Waters ×127
PDB id:
1j8g
Name: RNA
Title: X-ray analysis of a RNA tetraplex r(uggggu)4 at ultra-high r
Structure: 5'-r( Up Gp Gp Gp Gp U)-3'. Chain: a, b, c, d. Engineered: yes
Source: Synthetic: yes
Biol. unit: Octamer (from PDB file)
Resolution:
0.61Å     R-factor:   not given     R-free:   0.112
Authors: J.Deng,Y.Xiong,M.Sundaralingam
Key ref:
J.Deng et al. (2001). X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 A). Proc Natl Acad Sci U S A, 98, 13665-13670. PubMed id: 11707581 DOI: 10.1073/pnas.241374798
Date:
21-May-01     Release date:   23-Nov-01    
 Headers
 References

 

 
DOI no: 10.1073/pnas.241374798 Proc Natl Acad Sci U S A 98:13665-13670 (2001)
PubMed id: 11707581  
 
 
X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 A).
J.Deng, Y.Xiong, M.Sundaralingam.
 
  ABSTRACT  
 
Four-stranded guanine tetraplexes in RNA have been identified to be involved in crucial biological functions, such as dimerization of retroviral RNA, translational repression, and mRNA turnover. However, the structural basis for these biological processes is still largely unknown. Here we report the RNA tetraplex structure (UGGGGU)(4) at ultra-high resolution (0.61 A). The space group is P42(1)2, and cell constants are a = b = 36.16 A and c = 74.09 A. The structure was solved by the multiple-wavelength anomalous dispersion method using a set of three-wavelength data of the isomorphous bromo derivative (br)UGGGGU and refined to 0.61-A resolution. Each of the four strands in the asymmetric unit forms a parallel tetraplex with symmetry-related molecules. The tetraplex molecules stack on one another in opposite polarity (head-to-head or tail-to-tail) to form a pseudocontinuous column. All of the 5'-end uridines rotate around the backbone of G2, swing out, and form unique octaplexes with the neighboring G tetraplexes, whereas the 3'-end uridines are stacked-in and form uridine tetrads. All of the bases are anti, and the riboses are in the mixed C2'- and C3'-puckering mode. Strontium ions are observed in every other guanine tetrad plane, sitting on the fourfold axis and associated to the eight O6 atoms of neighboring guanine bases in a bipyramidal-antiprism geometry. The hydrogens are clearly observed in the structure.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. The coordination geometries of the metal ions and the spermine molecule. (a) The Sr2+ ion (purple) is coordinated to eight guanine O6 atoms. (b) Three Ca^2+ ions are coordinated to U6 (Ca1), U7 (Ca2), and U12 (Ca3) residues, respectively. (c) Coordination of the spermine molecule (blue) in stereoview. Hydrogen bonds are shown in white dashed lines. Individual RNA strands are depicted in different colors.
Figure 7.
Fig. 7. Hydrogen bonding in the G and U tetrads. The 2F[o] F[c] maps are calculated at 2 level and shown in blue. Top views are shown in the upper row and side views in the lower row. (a and b) G tetrads. The guanines are hydrogen bonded to each other by clockwise Hoogsteen-like pairing (N1H O4) with near ideal planarity. (c and d) The U6/U12 tetrad. It is formed with a single hydrogen bond between N3 and O4 atoms in a counterclockwise pattern. (e and f) The U24 tetrad is flipped over in a clockwise N3-H---O4 hydrogen-bonding pattern.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20571083 D.Gomez, A.Guédin, J.L.Mergny, B.Salles, J.F.Riou, M.P.Teulade-Fichou, and P.Calsou (2010).
A G-quadruplex structure within the 5'-UTR of TRF2 mRNA represses translation in human cells.
  Nucleic Acids Res, 38, 7187-7198.  
20413582 G.W.Collie, S.M.Haider, S.Neidle, and G.N.Parkinson (2010).
A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex.
  Nucleic Acids Res, 38, 5569-5580.
PDB code: 3ibk
19943071 T.van der Wijst, B.Lippert, M.Swart, C.F.Guerra, and F.M.Bickelhaupt (2010).
Differential stabilization of adenine quartets by anions and cations.
  J Biol Inorg Chem, 15, 387-397.  
19823751 J.M.Lipay, and M.R.Mihailescu (2009).
NMR spectroscopy and kinetic studies of the quadruplex forming RNA r(UGGAGGU).
  Mol Biosyst, 5, 1347-1355.  
19436709 J.Tan, C.Vonrhein, O.S.Smart, G.Bricogne, M.Bollati, Y.Kusov, G.Hansen, J.R.Mesters, C.L.Schmidt, and R.Hilgenfeld (2009).
The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes.
  PLoS Pathog, 5, e1000428.
PDB codes: 2w2g 2wct
19690373 M.J.Schnieders, T.D.Fenn, V.S.Pande, and A.T.Brunger (2009).
Polarizable atomic multipole X-ray refinement: application to peptide crystals.
  Acta Crystallogr D Biol Crystallogr, 65, 952-965.  
18096613 B.Puffer, H.Moroder, M.Aigner, and R.Micura (2008).
2'-Methylseleno-modified oligoribonucleotides for X-ray crystallography synthesized by the ACE RNA solid-phase approach.
  Nucleic Acids Res, 36, 970-983.  
18991403 S.Kumari, A.Bugaut, and S.Balasubramanian (2008).
Position and stability are determining factors for translation repression by an RNA G-quadruplex-forming sequence within the 5' UTR of the NRAS proto-oncogene.
  Biochemistry, 47, 12664-12669.  
17242509 A.Volkov, M.Messerschmidt, and P.Coppens (2007).
Improving the scattering-factor formalism in protein refinement: application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures.
  Acta Crystallogr D Biol Crystallogr, 63, 160-170.  
17505106 C.Creze, B.Rinaldi, R.Haser, P.Bouvet, and P.Gouet (2007).
Structure of a d(TGGGGT) quadruplex crystallized in the presence of Li+ ions.
  Acta Crystallogr D Biol Crystallogr, 63, 682-688.
PDB code: 2o4f
17452355 C.M.Barbieri, A.R.Srinivasan, S.G.Rzuczek, J.E.Rice, E.J.LaVoie, and D.S.Pilch (2007).
Defining the mode, energetics and specificity with which a macrocyclic hexaoxazole binds to human telomeric G-quadruplex DNA.
  Nucleic Acids Res, 35, 3272-3286.  
17913750 D.J.Patel, A.T.Phan, and V.Kuryavyi (2007).
Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.
  Nucleic Acids Res, 35, 7429-7455.  
17013819 I.V.Smirnov, and R.H.Shafer (2007).
Electrostatics dominate quadruplex stability.
  Biopolymers, 85, 91.  
17656312 M.Wieland, and J.S.Hartig (2007).
RNA quadruplex-based modulation of gene expression.
  Chem Biol, 14, 757-763.  
16492787 B.Pan, K.Shi, and M.Sundaralingam (2006).
Base-tetrad swapping results in dimerization of RNA quadruplexes: implications for formation of the i-motif RNA octaplex.
  Proc Natl Acad Sci U S A, 103, 3130-3134.
PDB code: 2awe
16944520 L.Petraccone, E.Erra, A.Randazzo, and C.Giancola (2006).
Energetic aspects of locked nucleic acids quadruplex association and dissociation.
  Biopolymers, 83, 584-594.  
16538665 P.R.Majhi, and R.H.Shafer (2006).
Characterization of an unusual folding pattern in a catalytically active guanine quadruplex structure.
  Biopolymers, 82, 558-569.  
17012276 S.Burge, G.N.Parkinson, P.Hazel, A.K.Todd, and S.Neidle (2006).
Quadruplex DNA: sequence, topology and structure.
  Nucleic Acids Res, 34, 5402-5415.  
16699193 W.Rypniewski, M.Vallazza, M.Perbandt, S.Klussmann, L.J.Delucas, C.Betzel, and V.A.Erdmann (2006).
The first crystal structure of an RNA racemate.
  Acta Crystallogr D Biol Crystallogr, 62, 659-664.
PDB codes: 2g32 2gpm 2gq4 2gq5 2gq6 2gq7
15897459 B.Knobloch, W.Linert, and H.Sigel (2005).
Metal ion-binding properties of (N3)-deprotonated uridine, thymidine, and related pyrimidine nucleosides in aqueous solution.
  Proc Natl Acad Sci U S A, 102, 7459-7464.  
15642696 J.L.Mergny, A.De Cian, A.Ghelab, B.Saccà, and L.Lacroix (2005).
Kinetics of tetramolecular quadruplexes.
  Nucleic Acids Res, 33, 81-94.  
15648098 M.Meyer, A.Hocquet, and J.Sühnel (2005).
Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads.
  J Comput Chem, 26, 352-364.  
15630477 M.P.Robertson, H.Igel, R.Baertsch, D.Haussler, M.Ares, and W.G.Scott (2005).
The structure of a rigorously conserved RNA element within the SARS virus genome.
  PLoS Biol, 3, e5.
PDB code: 1xjr
16299826 M.Roitzsch, and B.Lippert (2005).
Inverting the charges of natural nucleobase quartets: a planar platinum-purine quartet with pronounced sulfate affinity.
  Angew Chem Int Ed Engl, 45, 147-150.  
  15562298 B.Pan, K.Shi, and M.Sundaralingam (2004).
Synthesis, Purification and Crystallization of Guanine-rich RNA Oligonucleotides.
  Biol Proced Online, 6, 257-262.  
14960719 C.Cáceres, G.Wright, C.Gouyette, G.Parkinson, and J.A.Subirana (2004).
A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions.
  Nucleic Acids Res, 32, 1097-1102.
PDB codes: 1s45 1s47
12842044 B.Pan, Y.Xiong, K.Shi, J.Deng, and M.Sundaralingam (2003).
Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: implications for specific binding in RNA tetraplexes.
  Structure, 11, 815-823.
PDB code: 1j6s
12842045 B.Pan, Y.Xiong, K.Shi, and M.Sundaralingam (2003).
An eight-stranded helical fragment in RNA crystal structure: implications for tetraplex interaction.
  Structure, 11, 825-831.
PDB code: 1mdg
14604532 B.Pan, Y.Xiong, K.Shi, and M.Sundaralingam (2003).
Crystal structure of a bulged RNA tetraplex at 1.1 a resolution: implications for a novel binding site in RNA tetraplex.
  Structure, 11, 1423-1430.
PDB code: 1p79
12872000 G.W.Han, M.L.Kopka, D.Langs, M.R.Sawaya, and R.E.Dickerson (2003).
Crystal structure of an RNA.DNA hybrid reveals intermolecular intercalation: dimer formation by base-pair swapping.
  Proc Natl Acad Sci U S A, 100, 9214-9219.
PDB code: 1jb8
12560479 J.H.Thorpe, S.C.Teixeira, B.C.Gale, and C.J.Cardin (2003).
Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution.
  Nucleic Acids Res, 31, 844-849.
PDB code: 1mf5
12467644 R.V.Guntaka, B.R.Varma, and K.T.Weber (2003).
Triplex-forming oligonucleotides as modulators of gene expression.
  Int J Biochem Cell Biol, 35, 22-31.  
11752559 H.Moine, and J.L.Mandel (2001).
Biomedicine. Do G quartets orchestrate fragile X pathology?
  Science, 294, 2487-2488.  
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 code is shown on the right.