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PDBsum entry 402d
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RNA PDB id
402d

 

 

 

 

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Contents
DNA/RNA
Waters ×30
PDB id:
402d
Name: RNA
Title: 5'-r( Cp Gp Cp Cp Ap Gp Cp G)-3'
Structure: RNA(5'-r( Cp Gp Cp Cp Ap Gp Cp G)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.207     R-free:   0.263
Authors: S.B.Jang,L.-W.Hung,Y.-I.Chi,E.L.Holbrook,R.Carter,S.R.Holbrook
Key ref:
S.B.Jang et al. (1998). Structure of an RNA internal loop consisting of tandem C-A+ base pairs. Biochemistry, 37, 11726-11731. PubMed id: 9718295 DOI: 10.1021/bi980758j
Date:
04-Jun-98     Release date:   16-Jun-98    
 Headers
 References

DNA/RNA chains
  C-G-C-C-A-G-C-G 8 bases
  C-G-C-C-A-G-C-G 8 bases

 

 
DOI no: 10.1021/bi980758j Biochemistry 37:11726-11731 (1998)
PubMed id: 9718295  
 
 
Structure of an RNA internal loop consisting of tandem C-A+ base pairs.
S.B.Jang, L.W.Hung, Y.I.Chi, E.L.Holbrook, R.J.Carter, S.R.Holbrook.
 
  ABSTRACT  
 
The crystal structure of the RNA octamer 5'-CGC(CA)GCG-3' has been determined from X-ray diffraction data to 2.3 A resolution. In the crystal, this oligomer forms a self-complementary double helix in the asymmetric unit. Tandem non-Watson-Crick C-A and A-C base pairs comprise an internal loop in the middle of the duplex, which is incorporated with little distortion of the A-form double helix. From the geometry of the C-A base pairs, it is inferred that the adenosine imino group is protonated and donates a hydrogen bond to the carbonyl group of the cytosine. The wobble geometry of the C-A+ base pairs is very similar to that of the common U-G non-Watson-Crick pair.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20554855 E.C.Magat Juan, S.Shimizu, X.Ma, T.Kurose, T.Haraguchi, F.Zhang, M.Tsunoda, A.Ohkubo, M.Sekine, T.Shibata, C.L.Millington, D.M.Williams, and A.Takénaka (2010).
Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one.
  Nucleic Acids Res, 38, 6737-6745.
PDB codes: 3n4n 3n4o
20139416 M.G.Gagnon, Y.I.Boutorine, and S.V.Steinberg (2010).
Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome.
  Nucleic Acids Res, 38, 3441-3453.  
19151083 C.Takemoto, L.L.Spremulli, L.A.Benkowski, T.Ueda, T.Yokogawa, and K.Watanabe (2009).
Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system.
  Nucleic Acids Res, 37, 1616-1627.  
19485416 G.Chen, S.D.Kennedy, and D.H.Turner (2009).
A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.
  Biochemistry, 48, 5738-5752.  
19715476 M.M.Islam, and G.Suresh Kumar (2009).
RNA-binding potential of protoberberine alkaloids: spectroscopic and calorimetric studies on the binding of berberine, palmatine, and coralyne to protonated RNA structures.
  DNA Cell Biol, 28, 637-650.  
16581850 S.B.Jang, L.W.Hung, M.S.Jeong, E.L.Holbrook, X.Chen, D.H.Turner, and S.R.Holbrook (2006).
The crystal structure at 1.5 angstroms resolution of an RNA octamer duplex containing tandem G.U basepairs.
  Biophys J, 90, 4530-4537.
PDB code: 2g3s
12777762 J.Deng, Y.Xiong, B.Pan, and M.Sundaralingam (2003).
Structure of an RNA dodecamer containing a fragment from SRP domain IV of Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 59, 1004-1011.
PDB code: 1lnt
12770867 K.Réblová, N.Spacková, R.Stefl, K.Csaszar, J.Koca, N.B.Leontis, and J.Sponer (2003).
Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.
  Biophys J, 84, 3564-3582.  
12361978 H.H.Bink, K.Hellendoorn, J.van der Meulen, and C.W.Pleij (2002).
Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA.
  Proc Natl Acad Sci U S A, 99, 13465-13470.  
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.  
12166647 S.Lima, J.Hildenbrand, A.Korostelev, S.Hattman, and H.Li (2002).
Crystal structure of an RNA helix recognized by a zinc-finger protein: an 18-bp duplex at 1.6 A resolution.
  RNA, 8, 924-932.
PDB code: 1kfo
  11780625 V.Ivanov, A.Beniaminov, A.Mikheyev, and E.Minyat (2001).
A mechanism for stop codon recognition by the ribosome: a bioinformatic approach.
  RNA, 7, 1683-1692.  
10668794 B.Masquida, and E.Westhof (2000).
On the wobble GoU and related pairs.
  RNA, 6, 9.  
10985772 N.Sugimoto, M.Nakano, and S.Nakano (2000).
Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes.
  Biochemistry, 39, 11270-11281.  
10917594 W.J.Melchers, J.M.Bakkers, H.J.Bruins Slot, J.M.Galama, V.I.Agol, and E.V.Pilipenko (2000).
Cross-talk between orientation-dependent recognition determinants of a complex control RNA element, the enterovirus oriR.
  RNA, 6, 976-987.  
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
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
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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