6VFF

Dimer of Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from human GLI1 gene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition.

Thuy-Boun, A.S.Thomas, J.M.Grajo, H.L.Palumbo, C.M.Park, S.Nguyen, L.T.Fisher, A.J.Beal, P.A.

(2020) Nucleic Acids Res 48: 7958-7972

  • DOI: https://doi.org/10.1093/nar/gkaa532
  • Primary Citation of Related Structures:  
    6VFF

  • PubMed Abstract: 

    Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine to inosine in duplex RNA, a modification that exhibits a multitude of effects on RNA structure and function. Recent studies have identified ADAR1 as a potential cancer therapeutic target. ADARs are also important in the development of directed RNA editing therapeutics. A comprehensive understanding of the molecular mechanism of the ADAR reaction will advance efforts to develop ADAR inhibitors and new tools for directed RNA editing. Here we report the X-ray crystal structure of a fragment of human ADAR2 comprising its deaminase domain and double stranded RNA binding domain 2 (dsRBD2) bound to an RNA duplex as an asymmetric homodimer. We identified a highly conserved ADAR dimerization interface and validated the importance of these sequence elements on dimer formation via gel mobility shift assays and size exclusion chromatography. We also show that mutation in the dimerization interface inhibits editing in an RNA substrate-dependent manner for both ADAR1 and ADAR2.


  • Organizational Affiliation

    Department of Chemistry, University of California, Davis, CA, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Double-stranded RNA-specific editase 1
A, B
488Homo 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*GP*AP*UP*AP*GP*CP*UP*AP*CP*G)-3)32Homo sapiens
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
RNA(5-R(*CP*GP*UP*AP*GP*CP*UP*AP*UP*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3)32Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170α = 90
b = 63.21β = 118.133
c = 142.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
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 StatesR01GM061115

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2020-08-26
    Changes: Database references, Derived calculations
  • Version 1.3: 2020-10-14
    Changes: Structure summary
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description