9Y4L: Human MDA5

CryoEM Structure of human MDA5 in complex with dsRNA (two protein subunits on dsRNA). Determined by electron microscopy at 2.96 Å resolution. Released 9 Sept 2026.

Method: Electron microscopy
Resolution: 2.96 Å
Organisms: Homo sapiens, in vitro transcription vector pT7-Fluc(deltai)
Chains: 4
Atoms: 12,044
Mol. weight: 187.6 kDa
Ligands: ANP
Released: 9 Sept 2026

Explore 9Y4L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y4L contains 71 α-helices and 56 β-strands across 2 chains. 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: 36 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	310-315	6
α-helix	317-321	5
β-strand	325-328	4	1
α-helix	335-352	18
β-strand	359-363	5	1
α-helix	366-372	7
α-helix	373-377	5
α-helix	378-381	4
β-strand	387-390	4	1
α-helix	400-406	7
β-strand	409-413	5	1
α-helix	414-422	9
α-helix	434-436	3
β-strand	439-443	5	1
α-helix	445-447	3
α-helix	453-474	22
α-helix	478-480	3
β-strand	483-488	6	1
α-helix	499-512	14
β-strand	517-519	3	1
α-helix	525-531	7
α-helix	535	1
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	619-638	20
α-helix	671-691	21
α-helix	699-713	15
β-strand	721-724	4	2
α-helix	728-740	13
α-helix	742-747	6
β-strand	751-754	4	2
α-helix	764-767	4
α-helix	768-779	12
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
β-strand	920-923	4	5
β-strand	927-930	4	5
α-helix	933-936	4
β-strand	940-941	2	5
β-strand	959-961	3	5
β-strand	967-973	7	5
β-strand	978-982	5	5
α-helix	984-986	3
β-strand	987-991	5	4
β-strand	997-998	2	4
α-helix	1003-1005	3
β-strand	1008	1	3
α-helix	1011	1
β-strand	1012	1	5
α-helix	1013-1014	2

Chain G: 35 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	310-314	5
α-helix	317-320	4
β-strand	325-328	4	6
α-helix	335-352	18
β-strand	359-363	5	6
α-helix	366-372	7
α-helix	373-377	5
α-helix	378-381	4
β-strand	387-390	4	6
α-helix	400-404	5
β-strand	409-413	5	6
α-helix	414-421	8
β-strand	439-443	5	6
α-helix	445-447	3
α-helix	453-473	21
β-strand	483-488	6	6
α-helix	499-512	14
β-strand	517-519	3	6
α-helix	525-531	7
α-helix	535	1
β-strand	536-538	3	7
β-strand	541-542	2	8
α-helix	549-564	16
α-helix	572	1
α-helix	576-592	17
α-helix	595-616	22
α-helix	619-639	21
α-helix	671-681	11
α-helix	684-691	8
α-helix	694-696	3
α-helix	699-714	16
β-strand	721-724	4	7
α-helix	728-740	13
α-helix	742-747	6
β-strand	751-754	4	7
α-helix	768-779	12
β-strand	787-790	4	7
β-strand	803-807	5	7
α-helix	813-822	10
β-strand	829-833	5	7
β-strand	834-835	2	8
α-helix	842-862	21
α-helix	866-884	19
α-helix	888-893	6
β-strand	897	1	9
α-helix	900-902	3
β-strand	903-907	5	10
β-strand	913-916	4	10
β-strand	920-923	4	11
β-strand	927-930	4	11
α-helix	933-938	6
β-strand	940-941	2	12
β-strand	959-961	3	12
β-strand	967-970	4	12
β-strand	971-974	4	13
β-strand	977-980	4	13
β-strand	981	1	11
α-helix	984-986	3
β-strand	987-991	5	10
β-strand	997-998	2	10
α-helix	1003-1005	3
β-strand	1008	1	9
α-helix	1011	1
β-strand	1012	1	11
α-helix	1013-1014	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interferon-induced helicase C domain-containing protein 1	A, G	protein	728	Homo sapiens	Q9BYX4 (AlphaFold model)
RNA (30-mer)	B	RNA	30	in vitro transcription vector pT7-Fluc(deltai)
RNA (30-mer)	C	RNA	30	in vitro transcription vector pT7-Fluc(deltai)

Sequence of entity 1 (A, G), FASTA

>9Y4L_1 Interferon-induced helicase C domain-containing protein 1 (chains A, G)
ARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPG
KVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQIL
ENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKP
VIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCK
KFAIADATREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKE
RVCAEHLRKYNEALQINDTIRMIDAYTHLETFYNEEKDKKFAVIEDDSDEGGDDEYCDGD
EDEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRNTIMEQYTRTEE
SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISK
FRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADESTYVLVAHSG
SGVIEHETVNDFREKMMYKAIHCVQNMKPEEYAHKILELQMQSIMEKKMKTKRNIAKHYK
NNPSLITFLCKNCSVLACSGEDIHVIEKMHHVNMTPEFKELYIVRENKALQKKCADYQIN
GEIICKCGQAWGTMMVHKGLDLPCLKIRNFVVVFKNNSTKKQYKKWVELPITFPNLDYSE
CCLFSDED

Sequence of entity 2 (B), FASTA

>9Y4L_2 RNA (30-MER) (chains B)
UUCGGUUAGGGGCUAGGACGAUAUUCAUUG

Sequence of entity 3 (C), FASTA

>9Y4L_3 RNA (30-MER) (chains C)
CAAUGAAUAUCGUCCUAGCCCCUAACCGAA

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	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…
9Y4J 2.81 Å, CryoEM Structure of human MDA5 with dsRNA (one protein subunit 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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