9OJV | pdb_00009ojv

Crystal structure of monoclonal J2 antibody bound to dsRNA

• PDB DOI: https://doi.org/10.2210/pdb9OJV/pdb
• NAKB: 9OJV

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Mus musculus, synthetic construct
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2025-05-08 Released: 2025-12-10 
• Deposition Author(s): Bou-Nader, C., Zhang, J.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.262 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Structural basis of double-stranded RNA recognition by the J2 monoclonal antibody.

Bou-Nader, C., Juma, K.M., Bothra, A., Brasington, A.J., Ghirlando, R., Suzuki, M., Garboczi, D.N., Leppla, S.H., Zhang, J.

(2025) Nat Commun 17: 635-635

• PubMed: 41390480 
• DOI: https://doi.org/10.1038/s41467-025-67414-z
• Primary Citation Related Structures: 
  9OJV


• PubMed Abstract: 
  

  Double-stranded (ds) RNAs are major structural components of the transcriptome, hallmarks of viral infection, and primary triggers of innate immune responses. The J2 monoclonal antibody is the gold-standard method to discover and map endogenous dsRNAs across subcellular locations and cell surfaces, detect exogenous RNAs in viral infection, and surveil mRNA prophylactics and therapeutics for inflammatory dsRNAs. To define its epitope, specificity, and mechanism, we determine a 2.85 Å co-crystal structure of J2 antigen-binding fragment (Fab) bound to dsRNA. J2 uses its heavy and light chains in tandem to track the dsRNA minor groove, recognizing a staggered 8-bp duplex. J2 is highly selective for dsRNAs, requires 14 bp for robust binding, and exhibits greatly diminished binding for GC-rich dsRNAs. J2 and the R-loop-specific S9.6 antibody share a common recognition strategy distinct from intracellular dsRNA-binding proteins. This study provides mechanistic insights into dsRNA recognition and establishes a framework for reliable application and data interpretation of the J2 antibody in RNA discovery.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
Laboratory of Parasitic Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
Protein & Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA.
Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
Laboratory of Parasitic Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA. [e-mail].
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 113.56 kDa 
• Atom Count: 7,309 
• Modeled Residue Count: 895 
• Deposited Residue Count: 946 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
J2 Fab heavy chain	A [auth C], C [auth A]	230	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
J2 Fab light chain	B [auth D], D [auth B]	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA strand1	E	24	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA strand2	F	24	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	G [auth C], H [auth C], I [auth C], J [auth D], K [auth D], L [auth A], M [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.262 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.391	α = 90
b = 92.374	β = 90
c = 194.663	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Bou-Nader, C., Zhang, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release
  
• Version 1.1: 2026-03-25
  Changes: Database references