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PDBsum entry 3k1v
Go to PDB code: 
dna_rna ligands metals links
RNA PDB id
3k1v

 

 

 

 

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JSmol PyMol  
Contents
DNA/RNA
Ligands
PRF
Metals
_CA ×4
Waters ×62
PDB id:
3k1v
Name: RNA
Title: Cocrystal structure of a mutant class-i preq1 riboswitch
Structure: Preq1 riboswitch. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: chemically synthesized RNA corresponding to a mutant of the natural sequence from bacillus subtilis
Resolution:
2.20Å     R-factor:   0.230     R-free:   0.269
Authors: D.J.Klein,T.E.Edwards,A.R.Ferre-D'Amare
Key ref:
D.J.Klein et al. (2009). Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat Struct Biol, 16, 343-344. PubMed id: 19234468 DOI: 10.1038/nsmb.1563
Date:
28-Sep-09     Release date:   06-Oct-09    
Supersedes: 3fu4
 Headers
 References

DNA/RNA chain
  A-G-A-G-G-U-U-C-U-A-G-C-C-C-C-U-C-U-A-U-A-A-A-A-A-A-C-U-A-A 30 bases

 

 
DOI no: 10.1038/nsmb.1563 Nat Struct Biol 16:343-344 (2009)
PubMed id: 19234468  
 
 
Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase.
D.J.Klein, T.E.Edwards, A.R.Ferré-D'Amaré.
 
  ABSTRACT  
 
Riboswitches are mRNA domains that bind metabolites and modulate gene expression in cis. We report cocrystal structures of a remarkably compact riboswitch (34 nucleotides suffice for ligand recognition) from Bacillus subtilis that is selective for the essential nucleobase preQ(1) (7-aminomethyl-7-deazaguanine). The structures reveal a previously unrecognized pseudoknot fold and suggest a conserved gene-regulatory mechanism whereby ligand binding promotes sequestration of an RNA segment that otherwise assembles into a transcriptional antiterminator.
 
  Selected figure(s)  
 
Figure 1.
(a) Secondary structure. Thin lines denote connectivity; outlined letters denote disordered nucleotides (base-pairing symbols follow those of ref. 14). Not shown are tertiary interactions between S1 and L3. (b) Structure cartoon. Gray, yellow and red spheres depict the disordered portion of L2, Ca^2+ and water, respectively. (c) Select L3 tertiary interactions. (d) Partially hydrated Ca^2+ ions stabilize the L1 turn. a and b depict the wild-type^2 structure, and c and d depict the sequence variant^4. 		Figure 2.
(a) Phylogenetically conserved^2 binding pocket. (b) In-line probing data^2 mapped onto the structure. Nucleotides with reduced scission in the presence of preQ[1] are colored blue. Crystallographically disordered C12 and U13 (red spheres) show increased scission in the presence of preQ[1] (ref. 2). (c) Gene regulation. In the absence of preQ[1], one S2 strand (pink) instead forms part of an antiterminator. PreQ[1] stabilizes S2 and allows formation of the terminator. a and b depict the sequence variant^4 and wild-type^2 structures, respectively.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 343-344) copyright 2009.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21240270 T.R.Blower, X.Y.Pei, F.L.Short, P.C.Fineran, D.P.Humphreys, B.F.Luisi, and G.P.Salmond (2011).
A processed noncoding RNA regulates an altruistic bacterial antiviral system.
  Nat Struct Mol Biol, 18, 185-190.
PDB codes: 2xd0 2xdb
20822574 A.R.Ferré-D'Amaré (2010).
The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA.
  Q Rev Biophys, 43, 423-447.  
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.  
  20495679 B.Liu, D.H.Mathews, and D.H.Turner (2010).
RNA pseudoknots: folding and finding.
  F1000 Biol Rep, 2, 8.  
19969538 J.M.Kelley, and D.Hamelberg (2010).
Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch.
  Nucleic Acids Res, 38, 1392-1400.  
20435898 M.Y.Chou, S.C.Lin, and K.Y.Chang (2010).
Stimulation of -1 programmed ribosomal frameshifting by a metabolite-responsive RNA pseudoknot.
  RNA, 16, 1236-1244.  
19948769 N.Kulshina, T.E.Edwards, and A.R.Ferré-D'Amaré (2010).
Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch.
  RNA, 16, 186-196.
PDB code: 3k0j
20100813 S.Cao, D.P.Giedroc, and S.J.Chen (2010).
Predicting loop-helix tertiary structural contacts in RNA pseudoknots.
  RNA, 16, 538-552.  
20534493 U.Rieder, C.Kreutz, and R.Micura (2010).
Folding of a transcriptionally acting preQ1 riboswitch.
  Proc Natl Acad Sci U S A, 107, 10804-10809.  
19843610 B.Puffer, C.Kreutz, U.Rieder, M.O.Ebert, R.Konrat, and R.Micura (2009).
5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy.
  Nucleic Acids Res, 37, 7728-7740.  
19898478 N.Kulshina, N.J.Baird, and A.R.Ferré-D'Amaré (2009).
Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch.
  Nat Struct Mol Biol, 16, 1212-1217.
PDB code: 3iwn
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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