PDBsum entry 1xjr

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dna_rna metals links
_MG ×2
Waters ×11
PDB id:
Name: RNA
Title: The structure of a rigorously conserved RNA element within the sars virus genome
Structure: S2m RNA. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: in vitro transcription from t7 RNA polymerase and DNA template
2.70Å     R-factor:   0.233     R-free:   0.243
Authors: M.P.Robertson,H.Igel,R.Baertsch,D.Haussler,M.Ares Jr., W.G.Scott
Key ref: M.P.Robertson et al. (2005). The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol, 3, e5-94. PubMed id: 15630477
24-Sep-04     Release date:   01-Feb-05    


PLoS Biol 3:e5-94 (2005)
PubMed id: 15630477  
The structure of a rigorously conserved RNA element within the SARS virus genome.
M.P.Robertson, H.Igel, R.Baertsch, D.Haussler, M.Ares, W.G.Scott.
We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m) RNA element of the SARS virus genome to 2.7-A resolution. SARS and related coronaviruses and astroviruses all possess a motif at the 3' end of their RNA genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable RNA genome. We find that this extreme conservation is clearly explained by the requirement to form a highly structured RNA whose unique tertiary structure includes a sharp 90 degrees kink of the helix axis and several novel longer-range tertiary interactions. The tertiary base interactions create a tunnel that runs perpendicular to the main helical axis whose interior is negatively charged and binds two magnesium ions. These unusual features likely form interaction surfaces with conserved host cell components or other reactive sites required for virus function. Based on its conservation in viral pathogen genomes and its absence in the human genome, we suggest that these unusual structural features in the s2m RNA element are attractive targets for the design of anti-viral therapeutic agents. Structural genomics has sought to deduce protein function based on three-dimensional homology. Here we have extended this approach to RNA by proposing potential functions for a rigorously conserved set of RNA tertiary structural interactions that occur within the SARS RNA genome itself. Based on tertiary structural comparisons, we propose the s2m RNA binds one or more proteins possessing an oligomer-binding-like fold, and we suggest a possible mechanism for SARS viral RNA hijacking of host protein synthesis, both based upon observed s2m RNA macromolecular mimicry of a relevant ribosomal RNA fold.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20049590 K.Sivaprakasam, O.R.Pagán, and G.P.Hess (2010).
Minimal RNA aptamer sequences that can inhibit or alleviate noncompetitive inhibition of the muscle-type nicotinic acetylcholine receptor.
  J Membr Biol, 233, 1.  
  21063474 P.L.Quan, C.Firth, C.Street, J.A.Henriquez, A.Petrosov, A.Tashmukhamedova, S.K.Hutchison, M.Egholm, M.O.Osinubi, M.Niezgoda, A.B.Ogunkoya, T.Briese, C.E.Rupprecht, and W.I.Lipkin (2010).
Identification of a severe acute respiratory syndrome coronavirus-like virus in a leaf-nosed bat in Nigeria.
  MBio, 1, 0.  
20195256 S.I.O'Donoghue, D.S.Goodsell, A.S.Frangakis, F.Jossinet, R.A.Laskowski, M.Nilges, H.R.Saibil, A.Schafferhans, R.C.Wade, E.Westhof, and A.J.Olson (2010).
Visualization of macromolecular structures.
  Nat Methods, 7, S42-S55.  
19279186 C.Hsiao, and L.D.Williams (2009).
A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center.
  Nucleic Acids Res, 37, 3134-3142.  
18971277 P.C.Woo, S.K.Lau, C.S.Lam, K.K.Lai, Y.Huang, P.Lee, G.S.Luk, K.C.Dyrting, K.H.Chan, and K.Y.Yuen (2009).
Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus.
  J Virol, 83, 908-917.  
18824509 M.Abraham, O.Dror, R.Nussinov, and H.J.Wolfson (2008).
Analysis and classification of RNA tertiary structures.
  RNA, 14, 2274-2289.  
18156685 M.Bartlam, X.Xue, and Z.Rao (2008).
The search for a structural basis for therapeutic intervention against the SARS coronavirus.
  Acta Crystallogr A, 64, 204-213.  
18566509 M.P.Robertson, and W.G.Scott (2008).
A general method for phasing novel complex RNA crystal structures without heavy-atom derivatives.
  Acta Crystallogr D Biol Crystallogr, 64, 738-744.  
16928755 S.G.Sawicki, D.L.Sawicki, and S.G.Siddell (2007).
A contemporary view of coronavirus transcription.
  J Virol, 81, 20-29.  
  15833113 C.J.Stark, and C.D.Atreya (2005).
Molecular advances in the cell biology of SARS-CoV and current disease prevention strategies.
  Virol J, 2, 35.  
15905274 F.Jossinet, and E.Westhof (2005).
Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure.
  Bioinformatics, 21, 3320-3321.  
16338414 H.Fan, A.Ooi, Y.W.Tan, S.Wang, S.Fang, D.X.Liu, and J.Lescar (2005).
The nucleocapsid protein of coronavirus infectious bronchitis virus: crystal structure of its N-terminal domain and multimerization properties.
  Structure, 13, 1859-1868.
PDB codes: 2btl 2bxx
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.