4IQS

RNA 8mer duplex modified with 4-Se-Uridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights of non-canonical U*U pair and Hoogsteen interaction probed with Se atom.

Sheng, J.Gan, J.Soares, A.S.Salon, J.Huang, Z.

(2013) Nucleic Acids Res. 41: 10476-10487

  • DOI: 10.1093/nar/gkt799

  • PubMed Abstract: 
  • Unlike DNA, in addition to the 2'-OH group, uracil nucleobase and its modifications play essential roles in structure and function diversities of non-coding RNAs. Non-canonical U•U base pair is ubiquitous in non-coding RNAs, which are highly diversif ...

    Unlike DNA, in addition to the 2'-OH group, uracil nucleobase and its modifications play essential roles in structure and function diversities of non-coding RNAs. Non-canonical U•U base pair is ubiquitous in non-coding RNAs, which are highly diversified. However, it is not completely clear how uracil plays the diversifing roles. To investigate and compare the uracil in U-A and U•U base pairs, we have decided to probe them with a selenium atom by synthesizing the novel 4-Se-uridine ((Se)U) phosphoramidite and Se-nucleobase-modified RNAs ((Se)U-RNAs), where the exo-4-oxygen of uracil is replaced by selenium. Our crystal structure studies of U-A and U•U pairs reveal that the native and Se-derivatized structures are virtually identical, and both U-A and U•U pairs can accommodate large Se atoms. Our thermostability and crystal structure studies indicate that the weakened H-bonding in U-A pair may be compensated by the base stacking, and that the stacking of the trans-Hoogsteen U•U pairs may stabilize RNA duplex and its junction. Our result confirms that the hydrogen bond (O4(…)H-C5) of the Hoogsteen pair is weak. Using the Se atom probe, our Se-functionalization studies reveal more insights into the U•U interaction and U-participation in structure and function diversification of nucleic acids.


    Organizational Affiliation

    Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA and Department of Biology, Brookhaven National Laboratory, Upton, NY, 11973, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*UP*GP*(S5)P*AP*CP*AP*C)-3')A,B,C,D,E,F8N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
US5
Query on US5
A, B, C, D, E, F
RNA LINKINGC9 H13 N2 O8 P SeU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.194 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 47.006α = 90.00
b = 47.006β = 90.00
c = 354.105γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release