9D5J

Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing deoxyinosine at the -1 position of the guide strand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
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Literature

Nucleoside Analogs in ADAR Guide Strands Enable Editing at 5'-G A Sites.

Manjunath, A.Cheng, J.Campbell, K.B.Jacobsen, C.S.Mendoza, H.G.Bierbaum, L.Jauregui-Matos, V.Doherty, E.E.Fisher, A.J.Beal, P.A.

(2024) Biomolecules 14

  • DOI: https://doi.org/10.3390/biom14101229
  • Primary Citation of Related Structures:  
    9D5J, 9D5K

  • PubMed Abstract: 

    Adenosine Deaminases Acting on RNA (ADARs) are members of a family of RNA editing enzymes that catalyze the conversion of adenosine into inosine in double-stranded RNA (dsRNA). ADARs' selective activity on dsRNA presents the ability to correct mutations at the transcriptome level using guiding oligonucleotides. However, this approach is limited by ADARs' preference for specific sequence contexts to achieve efficient editing. Substrates with a guanosine adjacent to the target adenosine in the 5' direction (5'-GA) are edited less efficiently compared to substrates with any other canonical nucleotides at this position. Previous studies showed that a G/purine mismatch at this position results in more efficient editing than a canonical G/C pair. Herein, we investigate a series of modified oligonucleotides containing purine or size-expanded nucleoside analogs on guide strands opposite the 5'-G (-1 position). The results demonstrate that modified adenosine and inosine analogs enhance editing at 5'-GA sites. Additionally, the inclusion of a size-expanded cytidine analog at this position improves editing over a control guide bearing cytidine. High-resolution crystal structures of ADAR:/RNA substrate complexes reveal the manner by which both inosine and size-expanded cytidine are capable of activating editing at 5'-GA sites. Further modification of these altered guide sequences for metabolic stability in human cells demonstrates that the incorporation of specific purine analogs at the -1 position significantly improves editing at 5'-GA sites.


  • 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
Isoform 4 of Double-stranded RNA-specific editase 1
A, B
487Homo sapiensMutation(s): 1 
Gene Names: ADARB1ADAR2DRADA2RED1
EC: 3.5.4.37
UniProt & NIH Common Fund Data Resources
Find proteins for P78563 (Homo sapiens)
Go to UniProtKB:  P78563
PHAROS:  P78563
GTEx:  ENSG00000197381 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78563-4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA Top Strand Containing 8-azanebularine (8AZ)32Homo sapiens
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA Bottom Strand containing deoxyinosine complementary to a guanosine adjacent to the target site32Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C],
K [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.694α = 90
b = 63.13β = 118.232
c = 141.778γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM149799
Other privateProQR

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release