1NAO

SOLUTION STRUCTURE OF AN RNA 2'-O-METHYLATED RNA DUPLEX CONTAINING AN RNA/DNA HYBRID SEGMENT AT THE CENTER, NMR, MINIMIZED AVERAGE STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: AVERAGED 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at the center.

Nishizaki, T.Iwai, S.Ohtsuka, E.Nakamura, H.

(1997) Biochemistry 36: 2577-2585

  • DOI: 10.1021/bi962297c

  • PubMed Abstract: 
  • The solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at its center, (ggagaugac).(GmUmCmATCTCmCm), where lowercase letters, capital letters, and capital letters with the subscript m are RNA, DNA, and ...

    The solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at its center, (ggagaugac).(GmUmCmATCTCmCm), where lowercase letters, capital letters, and capital letters with the subscript m are RNA, DNA, and 2'-O-methylated RNA residues, respectively, was determined by observing the NMR spectra and performing the full relaxation matrix refinement. The 2'-O-methylation gives several characteristic features to oligoribonucleotides. In addition, this hybrid duplex is cleaved at a specific position by Escherichia coli ribonuclease HI, and so the role of the tertiary structure during the substrate recognition by the enzyme is of interest. The NOE connectivities among the proton resonances revealed that the duplex was a right handed helix. The 2'-O-methylated RNA segments had a typical C3'-endo conformation, and the 2'-O-methyl groups were directed to the minor groove of this duplex, taking the torsion angles phi (C1'-C2'-02'-CH3) that were all gauche(+). The DNA residues in the central RNA.DNA hybrid duplex formed the C3'-endo conformation, except for the middle thymine residue. No remarkable structural discontinuities were observed around the junction sites at either the 5'- or 3'-end of the DNA. The overall structure was close to the typical A-form duplex.


    Organizational Affiliation

    Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*AP*GP*AP*UP*GP*AP*C)-3')A9N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA/RNA (5'-R(*OMGP*OMUP*OMC)-D(P*AP*TP*CP*T)-R(P*OMCP*OMC)-3')B9N/A
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
OMU
Query on OMU
B
RNA LINKINGC10 H15 N2 O9 PU
OMC
Query on OMC
B
RNA LINKINGC10 H16 N3 O8 PC
OMG
Query on OMG
B
RNA LINKINGC11 H16 N5 O8 PG
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: AVERAGED 
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-27
    Type: Initial release
  • Version 1.1: 2008-03-10
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance