9F2L | pdb_00009f2l

Cryo-EM structure of the I923V MDA5-dsRNA filament with ADP-AlF4 bound and 73-degree helical twist

• PDB DOI: https://doi.org/10.2210/pdb9F2L/pdb
• EM Map EMD-50150: EMDB EMDataResource
• NAKB: 9F2L

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


• Deposited: 2024-04-23 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.86 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: experimental

Literature

Molecular basis of autoimmune disease protection by MDA5 variants.

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

(2025) Cell Rep 44: 115754-115754

• PubMed: 40450684 
• DOI: https://doi.org/10.1016/j.celrep.2025.115754
• Primary Citation Related Structures: 
  9F0J, 9F1U, 9F20, 9F2L, 9F2W, 9F3P


• PubMed Abstract: 
  

  MDA5 recognizes double-stranded RNA (dsRNA) from viruses and retroelements. Cooperative filament formation and ATP-dependent proofreading confer MDA5 with the necessary sensitivity and specificity for dsRNA. Many MDA5 genetic variants are associated with protection from autoimmune disease while increasing the risk of infection and chronic inflammation. How these variants affect RNA sensing remains unclear. Here, we determine the consequences of autoimmune-protective variants on the molecular structure and activities of MDA5. Rare variants E627 ^∗ and I923V reduce the interferon response to picornavirus infection. E627 ^∗ does not bind RNA. I923V is ATPase hyperactive, causing premature dissociation from dsRNA. Cryoelectron microscopy (cryo-EM) structures of MDA5 I923V bound to dsRNA at different stages of ATP hydrolysis reveal smaller RNA binding interfaces, leading to excessive proofreading activity. Variants R843H and T946A, which are genetically linked and cause mild phenotypes, did not affect cytokine induction, suggesting an indirect disease mechanism. In conclusion, autoimmune-protective MDA5 variants dampen MDA5-dependent signaling via multiple mechanisms.

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Organizational Affiliation: 
• Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK; Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.
Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK.
Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK; Department of Genomes and Genetics, Institut Pasteur, 75724 Paris, France.
Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, the Netherlands.
Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.
Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK. Electronic address: [e-mail].

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: 126.22 kDa 
• Atom Count: 6,129 
• Modeled Residue Count: 714 
• Deposited Residue Count: 1,056 
• 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'-R(P*CP*AP*AP*GP*CP*CP*GP*AP*GP*GP*AP*GP*AP*G)-3')	B [auth X]	14	Mus musculus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*UP*CP*UP*CP*CP*UP*CP*GP*GP*CP*UP*UP*G)-3')	C [auth Y]	14	Mus musculus

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ALF (Subject of Investigation/LOI)	F [auth A]	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.86 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.

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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
  
• Version 1.1: 2025-06-18
  Changes: Data collection, Database references