9Y4L | pdb_00009y4l

CryoEM Structure of human MDA5 in complex with dsRNA (two protein subunits on dsRNA)

PDB DOI: https://doi.org/10.2210/pdb9Y4L/pdb
EM Map EMD-72485: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, in vitro transcription vector pT7-Fluc(deltai)
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-09-03 Released: 2026-09-09
Deposition Author(s): Xu, L., Chung, K., Pyle, A.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.96 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9Y4L

This is version 1.0 of the entry. See complete history.

Literature

Unraveling the molecular basis for MDA5 T331I disease-linked mutation

Xu, L., Chung, K., Guo, R., Pan, A., Pyle, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 187.6 kDa
Atom Count: 12,044
Modeled Residue Count: 1,388
Deposited Residue Count: 1,516
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-induced helicase C domain-containing protein 1	A, B [auth G]	728	Homo sapiens	Mutation(s): 0 Gene Names: IFIH1, MDA5, RH116 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYX4 (Homo sapiens) Explore Q9BYX4 Go to UniProtKB: Q9BYX4
PHAROS: Q9BYX4 GTEx: ENSG00000115267
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYX4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (30-MER)	C [auth B]	30	in vitro transcription vector pT7-Fluc(deltai)
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 3
RNA (30-MER)	D [auth C]	30	in vitro transcription vector pT7-Fluc(deltai)
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth G] MOL2 format, chain E [auth A] MOL2 format, chain F [auth G] mmCIF format, chain E [auth A] mmCIF format, chain F [auth G]	E [auth A], F [auth G]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth G] Interactions & Density Focus chain E [auth A] Focus chain F [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.96 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-09-09
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.