9F0J | pdb_00009f0j

Cryo-EM structure of the I923V MDA5-dsRNA filament without nucleotide

• PDB DOI: https://doi.org/10.2210/pdb9F0J/pdb
• EM Map EMD-50111: EMDB EMDataResource
• NAKB: 9F0J

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-04-16 Released: 2025-02-26 
• Deposition Author(s): Singh, R., Herrero del Valle, A., Modis, Y.
• Funding Organization(s): Wellcome Trust, Human Frontier Science Program (HFSP)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: experimental

Literature

Molecular basis of autoimmune disease protection by MDA5 variants

Singh, R., Herrero del Valle, A., Joiner, J.D., Zwaagstra, M., Ferguson, B.J., van Kuppeveld, F.J.M., Modis, Y.

(2024) bioRxiv 

• DOI: https://doi.org/10.1101/2024.10.03.616466

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 126.32 kDa 
• Atom Count: 5,782 
• Modelled Residue Count: 670 
• Deposited Residue Count: 1,058 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-induced helicase C domain-containing protein 1	A	1,028	Mus musculus	Mutation(s): 1  Gene Names: Ifih1 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q8R5F7 (Mus musculus) Explore Q8R5F7  Go to UniProtKB:  Q8R5F7
IMPC:  MGI:1918836

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-UCCAUGCGCAUGACG-3')	B [auth X]	15	Mus musculus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-CGUCAUGCGCAUGGA-3')	C [auth Z]	15	Mus musculus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX	1.21

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Singh, R., Herrero del Valle, A., Modis, Y.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	101908/Z/13/Z
Wellcome Trust	United Kingdom	217191/Z/19/Z
Wellcome Trust	United Kingdom	215378/Z/19/Z
Human Frontier Science Program (HFSP)	France	LT000454/2021-L

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release