165D

THE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RESOLUTION AND IMPLICATIONS FOR THE PREDICTION OF RNA SECONDARY STRUCTURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure.

Cruse, W.B.Saludjian, P.Biala, E.Strazewski, P.Prange, T.Kennard, O.

(1994) Proc.Natl.Acad.Sci.USA 91: 4160-4164


  • PubMed Abstract: 
  • The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6Cl3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to ...

    The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6Cl3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to a resolution of 1.6 A, indicates an eight-base-pair A-RNA duplex containing a central block of two G.U and two C.U pairs. Self-pairs which approximate to Watson-Crick geometry are also formed in the extended crystal structure between symmetry-related BrU residues and are part of infinite double-helical stacks. The G.U pair is a wobble base pair analogous to the G.T pair found in DNA fragments. The C.U mismatch involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit of the base pair in the RNA helix. The BrU.BrU pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry. The structure observed within the crystal has some parallels with the structure of globular RNAs, and the presence of stable, noncanonical base pairs has implications for the prediction of RNA secondary structure.


    Organizational Affiliation

    Cambridge Crystallographic Data Centre, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA/RNA (5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BRU))-3')A,B9N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RHD
Query on RHD

Download SDF File 
Download CCD File 
A, B
RHODIUM HEXAMINE ION
H18 N6 Rh
JGYYKTIOJIEIKU-QTRIFGRDAZ
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
A, B
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Work: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 53.800α = 90.00
b = 19.400β = 109.90
c = 50.140γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-18
    Type: Data collection