9B89 | pdb_00009b89

Cryo-EM structure of human ADAR1 in complex with dsRNA derived from HT2C gene in the pre-editing state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Biochemical profiling and structural basis of ADAR1-mediated RNA editing.

Deng, X.Sun, L.Zhang, M.Basavaraj, R.Wang, J.Weng, Y.L.Gao, Y.

(2025) Mol Cell 85: 1381-1394.e6

  • DOI: https://doi.org/10.1016/j.molcel.2025.02.017
  • Primary Citation of Related Structures:  
    9B83, 9B84, 9B89

  • PubMed Abstract: 

    ADAR1 regulates RNA-induced immune responses by converting adenosine to inosine in double-stranded RNA. Mutations in ADAR1 are associated with human autoimmune disease, and targeting ADAR1 has been proposed for cancer immunotherapy. However, the molecular mechanisms underlying ADAR1-mediated editing remain unclear. Here, we provide detailed biochemical and structural characterizations of human ADAR1. Our biochemical profiling reveals that ADAR1 editing is both sequence and RNA-duplex-length dependent but can well tolerate mismatches near the editing site. High-resolution ADAR1-RNA complex structures, combined with mutagenesis, elucidate RNA binding, substrate selection, dimerization, and the essential role of RNA-binding domain 3. The ADAR1 structures also help explain the potential defects of disease-associated mutations, where biochemical and RNA sequencing analysis further indicate some of the mutations preferentially impact the editing of RNAs with short duplexes. These findings unveil the molecular basis of ADAR1 editing and provide insights into its immune-regulatory functions and therapeutic potential.


  • Organizational Affiliation
    • Department of Biosciences, Rice University, Houston, TX 77005, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein,Double-stranded RNA-specific adenosine deaminase
A, B
1,492Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
EC: 3.5.4.37
UniProt & NIH Common Fund Data Resources
Find proteins for P55265 (Homo sapiens)
Explore P55265 
Go to UniProtKB:  P55265
PHAROS:  P55265
GTEx:  ENSG00000160710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55265
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (71-MER)71Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP190602

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-16
    Changes: Data collection, Database references