2AO5

Crystal structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G-U base pairs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G.U base pairs.

Utsunomiya, R.Suto, K.Balasundaresan, D.Fukamizu, A.Kumar, P.K.Mizuno, H.

(2006) Acta Crystallogr.,Sect.D 62: 331-338

  • DOI: 10.1107/S0907444905043210

  • PubMed Abstract: 
  • The crystal structure of a self-complementary RNA duplex r(GGCG(Br)UGCGCU)(2) with terminal G.U and internal tandem G.U base pairs has been determined at 2.1 Angstroms resolution. The crystals belong to the tetragonal space group P4(3), with unit-cel ...

    The crystal structure of a self-complementary RNA duplex r(GGCG(Br)UGCGCU)(2) with terminal G.U and internal tandem G.U base pairs has been determined at 2.1 Angstroms resolution. The crystals belong to the tetragonal space group P4(3), with unit-cell parameters a = b = 37.69, c = 96.28 Angstroms and two duplexes in the asymmetric unit. The two strands of each duplex are related by a pseudodyad axis. The structure was refined to final R(work) and R(free) values of 20.9 and 25.3%, respectively. The duplexes stack in an end-to-end manner, forming infinite columns along the c axis. This is the first structural study of an RNA duplex containing G.U pairs at the termini. The stacking overlaps of the terminal G.U base pairs with their adjacent Watson-Crick base pairs are larger than those of Watson-Crick base pairs of the 5'-YR-3'/3'-RY-5' type. The terminal G.U base pairs of neighbouring duplexes are also stacked with each other. An alternating underwound-overwound pattern of the twist angles is seen at each step along the duplex. This observation is typical for internal tandem G.U pairs, while the terminal G.U base pairs exhibit high twist angles with the adjacent Watson-Crick pairs. The 3'-side of U of the internal G.U base pair, which is unstacked, appears to be stabilized by pi-cation interaction with an Mg(2+) ion.


    Organizational Affiliation

    Institute of Applied Biochemistry, University of Tsukuba, Ibaraki, Japan.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'A,B,C,D10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5BU
Query on 5BU
A, B, C, D
RNA LINKINGC9 H12 Br N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 37.693α = 90.00
b = 37.693β = 90.00
c = 96.283γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance