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

Specificity and mechanism of the double-stranded RNA-specific 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.

To be published.

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