9Y4J: Human MDA5 with dsRNA

CryoEM Structure of human MDA5 with dsRNA (one protein subunit on dsRNA). Determined by electron microscopy at 2.81 Å resolution. Released 9 Sept 2026.

Method: Electron microscopy
Resolution: 2.81 Å
Organisms: Homo sapiens, in vitro transcription vector pT7-Fluc(deltai)
Chains: 3
Atoms: 5,943
Mol. weight: 92.55 kDa
Ligands: ANP, MG
Released: 9 Sept 2026

Explore 9Y4J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y4J contains 37 α-helices and 26 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 37 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	310-316	7
β-strand	325-328	4	1
α-helix	335-352	18
β-strand	359-363	5	1
α-helix	366-371	6
α-helix	372-377	6
α-helix	378-381	4
β-strand	387-390	4	1
α-helix	395-396	2
α-helix	400-406	7
β-strand	409-413	5	1
α-helix	414-421	8
α-helix	434-436	3
β-strand	439-443	5	1
α-helix	445-447	3
α-helix	453-472	20
β-strand	483-488	6	1
α-helix	499-512	14
β-strand	517-520	4	1
α-helix	525-531	7
α-helix	533-535	3
β-strand	536-542	7	2
α-helix	549-564	16
α-helix	572	1
α-helix	576-592	17
α-helix	595-616	22
α-helix	619-636	18
α-helix	671-681	11
α-helix	684-691	8
α-helix	694-696	3
α-helix	699-711	13
β-strand	721-724	4	2
α-helix	728-739	12
α-helix	742-746	5
β-strand	751-754	4	2
α-helix	764-767	4
α-helix	768-778	11
β-strand	787-790	4	2
β-strand	803-807	5	2
α-helix	813-820	8
β-strand	829-835	7	2
α-helix	840-862	23
α-helix	866-885	20
α-helix	888-893	6
β-strand	897	1	3
α-helix	900-902	3
β-strand	903-907	5	4
β-strand	913-916	4	4
α-helix	917-919	3
β-strand	920-923	4	5
β-strand	927-930	4	5
α-helix	933-936	4
β-strand	939-941	3	5
α-helix	958	1
β-strand	959-962	4	5
β-strand	967-974	8	5
β-strand	977-982	6	5
α-helix	983	1
α-helix	984-986	3
β-strand	987-991	5	4
β-strand	997-998	2	4
β-strand	1008	1	3
β-strand	1012	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interferon-induced helicase C domain-containing protein 1	A	protein	728	Homo sapiens	Q9BYX4 (AlphaFold model)
RNA 13mer	B	RNA	13	in vitro transcription vector pT7-Fluc(deltai)
RNA 13mer	C	RNA	13	in vitro transcription vector pT7-Fluc(deltai)

Sequence of entity 1 (A), FASTA

>9Y4J_1 Interferon-induced helicase C domain-containing protein 1 (chains A)
ARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPG
KVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQIL
ENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKP
VIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCK
KFAIADATREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKE
RVCAEHLRKYNEALQINDTIRMIDAYTHLETFYNEEKDKKFAVIEDDSDEGGDDEYCDGD
EDEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRNTIMEQYTRTEE
SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISK
FRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADESTYVLVAHSG
SGVIEHETVNDFREKMMYKAIHCVQNMKPEEYAHKILELQMQSIMEKKMKTKRNIAKHYK
NNPSLITFLCKNCSVLACSGEDIHVIEKMHHVNMTPEFKELYIVRENKALQKKCADYQIN
GEIICKCGQAWGTMMVHKGLDLPCLKIRNFVVVFKNNSTKKQYKKWVELPITFPNLDYSE
CCLFSDED

Sequence of entity 2 (B), FASTA

>9Y4J_2 RNA 13mer (chains B)
CGGUUAGGGGCUA

Sequence of entity 3 (C), FASTA

>9Y4J_3 RNA 13mer (chains C)
UAGCCCCUAACCG

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
MG	Magnesium ion	Mg	2

Primary citation

Unraveling the molecular basis for MDA5 T331I disease-linked mutation. Xu, L., Chung, K., Guo, R. et al. To be published.

Other PDB entries of the same protein (UniProt Q9BYX4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3GA3 1.45 Å, Crystal structure of the C-terminal domain of human MDA5
3B6E 1.6 Å, Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma…
9Y4L 2.96 Å, CryoEM Structure of human MDA5 in complex with dsRNA (two protein subunits on dsRNA)
9LOV 3.07 Å, LGP2:MDA5:dsRNA filament
9Q60 3.12 Å, CryoEM Structure of human MDA5 disease-linked mutant T331I with dsRNA (one protein…
7DNI 3.2 Å, MDA5 CARDs-MAVS CARD polyUb complex
9Q5W 3.21 Å, CryoEM Structure of human MDA5 T331I mutant in complex with dsRNA
7DNJ 3.3 Å, K63-polyUb MDA5CARDs complex
4GL2 3.56 Å, Structural Basis for dsRNA duplex backbone recognition by MDA5
7JL0 4.3 Å, Cryo-EM structure of MDA5-dsRNA in complex with TRIM65 PSpry domain (Monomer)
7JL2 4.3 Å, Cryo-EM structure of MDA5-dsRNA filament in complex with TRIM65 PSpry domain (Trimer)
2RQB Solution structure of MDA5 CTD

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