7JL2: MDA5-dsRNA filament

Cryo-EM structure of MDA5-dsRNA filament in complex with TRIM65 PSpry domain (Trimer). Determined by electron microscopy at 4.3 Å resolution. Released 9 Dec 2020.

Method: Electron microscopy
Resolution: 4.3 Å
Organism: Homo sapiens
Chains: 8
Atoms: 22,128
Mol. weight: 349.68 kDa
Ligands: MG, ALF, ADP, ZN
Released: 9 Dec 2020

Explore 7JL2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JL2 contains 98 α-helices and 135 β-strands across 6 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.

Chains A, C and E: 31 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	310-316	7
α-helix	318-320	3
β-strand	325-328	4	1
α-helix	335-353	19
β-strand	359-363	5	1
α-helix	366-372	7
α-helix	373-377	5
α-helix	378-381	4
β-strand	387-389	3	1
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	499-513	15
α-helix	525-531	7
α-helix	534-535	2
β-strand	536-542	7	2
α-helix	549-564	16
α-helix	576-592	17
α-helix	598-616	19
α-helix	619-639	21
α-helix	674-691	18
α-helix	699-715	17
β-strand	721-724	4	2
α-helix	728-740	13
α-helix	742-746	5
β-strand	751-754	4	2
α-helix	768-780	13
β-strand	785-788	4	2
α-helix	790-792	3
β-strand	803-807	5	2
α-helix	814-822	9
β-strand	829-835	7	2
α-helix	841-861	21
α-helix	866-894	29
β-strand	904-906	3	3
β-strand	913-916	4	3
α-helix	917-919	3
β-strand	920-923	4	4
β-strand	927-930	4	4
α-helix	933-938	6
β-strand	940-942	3	5
α-helix	958	1
β-strand	959-961	3	5
β-strand	967-970	4	5
β-strand	971-974	4	6
β-strand	977-980	4	6
β-strand	981	1	4
α-helix	984-986	3
β-strand	988-990	3	3
β-strand	997-998	2	3
β-strand	1012	1	4

Chain B: 1 helix, 20 β-strands

Element	Residues	Length	Sheet
α-helix	322-327	6
β-strand	330	1	7
β-strand	335	1	8
β-strand	344-347	4	7
β-strand	352-355	4	7
β-strand	372-374	3	9
β-strand	375	1	8
β-strand	379	1	10
β-strand	384-390	7	7
β-strand	395-400	6	9
β-strand	422-427	6	9
β-strand	431-435	5	9
β-strand	436	1	11
β-strand	439	1	11
β-strand	442-444	3	9
β-strand	451-456	6	7
β-strand	461-466	6	7
β-strand	472-478	7	7
β-strand	485	1	10
β-strand	486-490	5	9
β-strand	496-499	4	7

Chains D and F: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	322-326	5
α-helix	327-329	3
β-strand	330	1	18
β-strand	335	1	19
β-strand	344-347	4	18
β-strand	352-355	4	18
β-strand	372-374	3	20
β-strand	375	1	19
β-strand	379	1	21
β-strand	384-390	7	18
β-strand	395-400	6	20
β-strand	422-427	6	20
β-strand	431-433	3	20
β-strand	436	1	22
β-strand	439	1	22
β-strand	442-444	3	20
β-strand	451-456	6	18
β-strand	461-466	6	18
β-strand	472-478	7	18
β-strand	485	1	21
β-strand	486-490	5	20
β-strand	496-499	4	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA (44-mer)	X	RNA	44	Homo sapiens
RNA (44-mer)	Y	RNA	44	Homo sapiens
Interferon-induced helicase C domain-containing protein 1	A, C, E	protein	739	Homo sapiens	Q9BYX4 (AlphaFold model)
Tripartite motif-containing protein 65	B, D, F	protein	191	Homo sapiens	Q6PJ69 (AlphaFold model)

Sequence of entity 1 (X), FASTA

>7JL2_1 RNA (44-MER) (chains X)
GACUGACUGACUGAAGACUGACUGACUGAAGACUGACUGACUGA

Sequence of entity 2 (Y), FASTA

>7JL2_2 RNA (44-MER) (chains Y)
UCAGUCAGUCAGUCUUCAGUCAGUCAGUCUUCAGUCAGUCAGUC

Sequence of entity 3 (A, C, E), FASTA

>7JL2_3 Interferon-induced helicase C domain-containing protein 1 (chains A, C, E)
MGSDSDEENVAARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDH
LDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKS
CDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKL
KNNRLKKENKPVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLD
QLKNQIQEPCKKFAIADATREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQME
KKAAKEGNRKERVCAEHLRKYNEALQINDTIRMIDAYTHLETFYNEEKDKKFAVIEDDSD
EGGDDEYCDGDEDEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRN
TIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPM
TQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARAD
ESTYVLVAHSGSGVIERETVNDFREKMMYKAIHCVQNMKPEEYAHKILELQMQSIMEKKM
KTKRNIAKHYKNNPSLITFLCKNCSVLACSGEDIHVIEKMHHVNMTPEFKELYIVREKKT
LQKKCADYQINGEIICKCGQAWGTMMVHKGLDLPCLKIRNFVVVFKNNSTKKQYKKWVEL
PITFPNLDYSECCLFSDED

Sequence of entity 4 (B, D, F), FASTA

>7JL2_4 Tripartite motif-containing protein 65 (chains B, D, F)
LAPVPSTVCPLRRKLWQNYRNLTFDPVSANRHFYLSRQDQQVKHLRQSRGPGGPGSFELW
QVQCAQSFQAGHHYWEVRASDHSVTLGVSYPQLPRSRLGPHTDNIGRGPSSWGLCVQEDS
LQAWHNGEAQRLPGVSGRLLGMDLDLASGCLTFYSLEPQTQPLYTFHALFNQPLTPVFWL
LEGRTLTLCHQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
ALF	Tetrafluoroaluminate ion	Al F4	3
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3
ZN	Zinc ion	Zn	3

Primary citation

Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases. Kato, K., Ahmad, S., Zhu, Z. et al. Mol Cell (2021) 81:599-613.e8. DOI 10.1016/j.molcel.2020.11.047 · PubMed

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)
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)
2RQB Solution structure of MDA5 CTD

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