6D06

Human ADAR2d E488Y mutant complexed with dsRNA containing an abasic site opposite the edited base


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

A Bump-Hole Approach for Directed RNA Editing.

Monteleone, L.R.Matthews, M.M.Palumbo, C.M.Thomas, J.M.Zheng, Y.Chiang, Y.Fisher, A.J.Beal, P.A.

(2019) Cell Chem Biol 26: 269

  • DOI: https://doi.org/10.1016/j.chembiol.2018.10.025
  • Primary Citation of Related Structures:  
    6D06

  • PubMed Abstract: 

    Molecules capable of directing changes to nucleic acid sequences are powerful tools for molecular biology and promising candidates for the therapeutic correction of disease-causing mutations. However, unwanted reactions at off-target sites complicate their use. Here we report selective combinations of mutant editing enzyme and directing oligonucleotide. Mutations in human ADAR2 (adenosine deaminase acting on RNA 2) that introduce aromatic amino acids at position 488 reduce background RNA editing. This residue is juxtaposed to the nucleobase that pairs with the editing site adenine, suggesting a steric clash for the bulky mutants. Replacing this nucleobase with a hydrogen atom removes the clash and restores editing activity. A crystal structure of the E488Y mutant bound to abasic site-containing RNA shows the accommodation of the tyrosine side chain. Finally, we demonstrate directed RNA editing in vitro and in human cells using mutant ADAR2 proteins and modified guide RNAs with reduced off-target activity.


  • Organizational Affiliation

    Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Double-stranded RNA-specific editase 1
A, D
403Homo sapiensMutation(s): 1 
Gene Names: ADARB1ADAR2DRADA2RED1
EC: 3.5.4.37
UniProt & NIH Common Fund Data Resources
Find proteins for P78563 (Homo sapiens)
Explore P78563 
Go to UniProtKB:  P78563
PHAROS:  P78563
GTEx:  ENSG00000197381 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78563
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')23Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*NP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')23Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.68α = 90
b = 63.44β = 126.64
c = 132.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM061115

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 2.0: 2020-01-01
    Changes: Author supporting evidence, Polymer sequence
  • Version 2.1: 2020-09-30
    Changes: Derived calculations, Structure summary
  • Version 2.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description