1C4L

SOLUTION STRUCTURE OF AN RNA DUPLEX INCLUDING A C-U BASE-PAIR


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: SUMMATION OF TOTAL ENERGY (COVALENT GEOMETRY, NON-BOND ENERGY, DISTANCE AND DIHEDRAL ANGLE CONSTRAINTS) 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of an RNA duplex including a C-U base pair.

Tanaka, Y.Kojima, C.Yamazaki, T.Kodama, T.S.Yasuno, K.Miyashita, S.Ono, A.Ono, A.Kainosho, M.Kyogoku, Y.

(2000) Biochemistry 39: 7074-7080


  • PubMed Abstract: 
  • The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of (15)N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solut ...

    The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of (15)N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solution structure of the RNA oligomer, r[CGACUCAGG].r[CCUGCGUCG], it was found that a single C-U mismatch preferred being stacked in the duplex rather than being flipped-out even in solution. Moreover, it adopts an irregular geometry, where the amino nitrogen (N4) of the cytidine and keto-oxygen (O4) of the uridine are within hydrogen-bonding distance, as seen in crystals. To further prove the presence of a hydrogen bond in the C-U pair, we employed a point-labeled cytidine at the exocyclic amino nitrogen of the cytidine in the C-U pair. The temperature profile of its (15)N chemical shift showed a sigmoidal transition curve, indicating the presence of a hydrogen bond in the C-U pair in the duplex.


    Related Citations: 
    • Structure model and physicochemical properties of the C-U mismatch pair in the double stranded RNA in solution
      Tanaka, Y.,Kojima, C.,Yamazaki, T.,Kyogoku, Y.,Miyashita, S.,Ono, A.S.,Kainosho, M.
      (1997) Nucleic Acids Symp.Ser. 37: 271


    Organizational Affiliation

    Institute for Protein Research, Osaka University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*GP*AP*CP*UP*CP*AP*GP*G)-3')A9N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*UP*GP*CP*GP*UP*CP*G)-3')B9N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: SUMMATION OF TOTAL ENERGY (COVALENT GEOMETRY, NON-BOND ENERGY, DISTANCE AND DIHEDRAL ANGLE CONSTRAINTS) 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-09
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance