6I1V

Structure of the RNA duplex containing pseudouridine residue (5'-Cp(PSU)pG-3' sequence context)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.

Deb, I.Popenda, L.Sarzynska, J.Malgowska, M.Lahiri, A.Gdaniec, Z.Kierzek, R.

(2019) Sci Rep 9: 16278-16278

  • DOI: 10.1038/s41598-019-52637-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pseudouridine (Ψ) is the most common chemical modification present in RNA. In general, Ψ increases the thermodynamic stability of RNA. However, the degree of stabilization depends on the sequence and structural context. To explain experimentally obse ...

    Pseudouridine (Ψ) is the most common chemical modification present in RNA. In general, Ψ increases the thermodynamic stability of RNA. However, the degree of stabilization depends on the sequence and structural context. To explain experimentally observed sequence dependence of the effect of Ψ on the thermodynamic stability of RNA duplexes, we investigated the structure, dynamics and hydration of RNA duplexes with an internal Ψ-A base pair in different nearest-neighbor sequence contexts. The structures of two RNA duplexes containing 5'-GΨC/3'-CAG and 5'-CΨG/3'-GAC motifs were determined using NMR spectroscopy. To gain insight into the effect of Ψ on duplex dynamics and hydration, we performed molecular dynamics (MD) simulations of RNA duplexes with 5'-GΨC/3'-CAG, 5'-CΨG/3'-GAC, 5'-AΨU/3'-UAA and 5'-UΨA/3'-AAU motifs and their unmodified counterparts. Our results showed a subtle impact from Ψ modification on the structure and dynamics of the RNA duplexes studied. The MD simulations confirmed the change in hydration pattern when U is replaced with Ψ. Quantum chemical calculations showed that the replacement of U with Ψ affected the intrinsic stacking energies at the base pair steps depending on the sequence context. The calculated intrinsic stacking energies help to explain the experimentally observed sequence dependent changes in the duplex stability from Ψ modification.


    Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan, 48109, USA.,Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, Kolkata, 700009, West Bengal, India.,NanoBioMedical Centre, Adam Mickiewicz University, Umultowska 85, 61-614, Poznan, Poland.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. joanna.sarzynska@ibch.poznan.pl.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*CP*AP*CP*(PSU)P*GP*AP*GP*U)-3')A9synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*CP*UP*CP*AP*GP*UP*GP*A)-3')B9synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A
RNA LINKINGC9 H13 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
PolandUMO-2017/25/B/ST5/00971
ItalyS/IND 15-05
PolandUMO-2013/08/A/ST5/00295

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release