7DNJ: K63-polyUb MDA5CARDs complex

K63-polyUb MDA5CARDs complex. Determined by electron microscopy at 3.3 Å resolution. Released 13 Oct 2021.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 12
Atoms: 10,926
Mol. weight: 163.92 kDa
Released: 13 Oct 2021

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

Secondary structure: helices and β-sheets

7DNJ contains 81 α-helices and 55 β-strands across 12 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: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	7-17	11
α-helix	19-23	5
α-helix	28-34	7
α-helix	40-53	14
α-helix	56-67	12
α-helix	75-85	11
α-helix	90-95	6
α-helix	103-104	2
α-helix	105-128	24
α-helix	131-138	8
α-helix	146-155	10
α-helix	156-158	3
α-helix	160-171	12
α-helix	177-186	10
α-helix	191-198	8

Chain B: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	7-17	11
α-helix	19-23	5
α-helix	28-31	4
α-helix	32-34	3
α-helix	40-67	28
α-helix	75-85	11
α-helix	89-93	5
α-helix	99-101	3
α-helix	103-104	2
α-helix	105-120	16
α-helix	122-128	7
α-helix	135-140	6
α-helix	146-155	10
α-helix	160-170	11
α-helix	171-173	3
α-helix	177-187	11
α-helix	191-198	8

Chain C: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	7-17	11
α-helix	19-25	7
α-helix	28-31	4
α-helix	40-52	13
α-helix	54-67	14
α-helix	75-85	11
α-helix	89-95	7
α-helix	102-104	3
α-helix	105-120	16
α-helix	122-128	7
α-helix	131-133	3
α-helix	135-140	6
α-helix	146-155	10
α-helix	160-171	12
α-helix	177-187	11
α-helix	191-197	7

Chain D: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	28-34	7
α-helix	42-67	26
α-helix	75-85	11
α-helix	89-95	7
α-helix	102-104	3
α-helix	105-128	24
α-helix	131-133	3
α-helix	135-140	6
α-helix	146-155	10
α-helix	156-158	3
α-helix	160-171	12
α-helix	177-187	11
α-helix	191-198	8

Chain E: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	11	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
β-strand	43-45	3	1
β-strand	48-49	2	1
β-strand	55	1	2
β-strand	66-69	4	1

Chain F: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-33	11
β-strand	41-44	4	3
β-strand	55	1	4
β-strand	66-71	6	3

Chain G: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
α-helix	11	1
β-strand	12-15	4	5
β-strand	22	1	6
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-44	4	5
β-strand	49	1	5
α-helix	50-51	2
β-strand	55	1	6
α-helix	56-59	4
β-strand	66-71	6	5

Chain H: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	7
β-strand	12-16	5	7
β-strand	22	1	8
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-44	4	7
β-strand	49	1	7
β-strand	55	1	8
α-helix	56-59	4
β-strand	65-71	7	7

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interferon-induced helicase C domain-containing protein 1	A, B, C, D	protein	208	Homo sapiens	Q9BYX4 (AlphaFold model)
Ubiquitin	E, F, G, H, I, J, K, L	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7DNJ_1 Interferon-induced helicase C domain-containing protein 1 (chains A, B, C, D)
MSNGYSTDENFRYLISCFRARVKMYIQVEPVLDYLTFLPAEVKEQIQRTVATSGNMQAVE
LLLSTLEKGVWHLGWTREFVEALRRTGSPLAARYMNPELTDLPSPSFENAHDEYLQLLNL
LQPTLVDKLLVRDVLDKCMEEELLTIEDRNRIAAAENNGNESGVRELLKRIVQKENWFSA
FLNVLRQTGNNELVQELTGSDCSESNAE

Sequence of entity 2 (E, F, G, H, I, J, K, L), FASTA

>7DNJ_2 Ubiquitin (chains E, F, G, H, I, J, K, L)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Ordered assembly of the cytosolic RNA-sensing MDA5-MAVS signaling complex via binding to unanchored K63-linked poly-ubiquitin chains. Song, B., Chen, Y., Liu, X. et al. Immunity (2021) 54:2218. DOI 10.1016/j.immuni.2021.09.008 · 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
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

Browse structure collections

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