9OP3 | pdb_00009op3

Structure of Human ADAR2-R2D complexed with dsRNA containing 8-azaN and 2'-Deoxy-2'-fluorouridine

• PDB DOI: https://doi.org/10.2210/pdb9OP3/pdb

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2025-05-16 Released: 2025-10-08 
• Deposition Author(s): Campbell, K.B., Ouye, R.B., Wong, B.L., Jiang, A., Okada, K., McKenney, R.J., Fisher, A.J., Beal, P.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Control of ADAR2 Dimerization and RNA Editing Efficiency by Site-specific 2'-Fluoro Modification of Guide RNAs

Campbell, K.B., Ouye, R.B., Wong, B.L., Jiang, A., Okada, K., McKenney, R.J., Fisher, A.J., Beal, P.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.17 kDa 
• Atom Count: 8,083 
• Modeled Residue Count: 903 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-stranded RNA-specific editase 1	A, B	488	Homo sapiens	Mutation(s): 1  Gene Names: ADARB1, ADAR2, DRADA2, RED1 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 ID: 2
Molecule	Chains	Length	Organism	Image
RNA 32mer Top Strand	C	32	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA 32mer 2F Bottom Strand	D	32	Homo sapiens

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	E [auth A], K [auth B]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
ZN	F [auth A], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170	α = 90
b = 63.21	β = 118.13
c = 142.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Campbell, K.B., Ouye, R.B., Wong, B.L., Jiang, A., Okada, K., McKenney, R.J., Fisher, A.J., Beal, P.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM141907
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM149799

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release