4GL2: DsRNA duplex backbone recognition by MDA5

Structural Basis for dsRNA duplex backbone recognition by MDA5. Determined by X-ray diffraction at 3.56 Å resolution. Released 9 Jan 2013.

Method: X-ray diffraction
Resolution: 3.56 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,735
Mol. weight: 177.42 kDa
Ligands: ZN, ANP
Released: 9 Jan 2013

Explore 4GL2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GL2 contains 59 α-helices and 51 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: 29 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	310-320	11
β-strand	325-327	3	1
α-helix	335-353	19
β-strand	359	1	1
β-strand	362-363	2	1
α-helix	367-372	6
α-helix	373-377	5
α-helix	378-381	4
β-strand	387-390	4	1
α-helix	400-405	6
β-strand	409-413	5	1
α-helix	414-420	7
α-helix	434-436	3
β-strand	439-443	5	1
α-helix	445-447	3
β-strand	449	1	2
β-strand	452	1	2
α-helix	457-472	16
β-strand	483-487	5	1
α-helix	499-513	15
α-helix	525-531	7
α-helix	534-535	2
β-strand	536-542	7	3
α-helix	550-565	16
α-helix	576-592	17
α-helix	598-616	19
α-helix	619-637	19
α-helix	671-691	21
α-helix	705-714	10
β-strand	721-724	4	3
α-helix	728-739	12
β-strand	752-753	2	3
α-helix	765-767	3
α-helix	768-778	11
β-strand	787-789	3	3
β-strand	805-807	3	3
α-helix	813-820	8
β-strand	829-835	7	3
α-helix	841-860	20
α-helix	866-883	18
β-strand	903-907	5	4
β-strand	913-916	4	4
α-helix	917-919	3
β-strand	921-923	3	5
β-strand	927-929	3	5
α-helix	933-938	6
β-strand	940-941	2	5
β-strand	959-961	3	5
β-strand	967-971	5	5
β-strand	980-982	3	5
α-helix	984-986	3
β-strand	987-991	5	4
β-strand	996-998	3	4
α-helix	1003-1005	3
β-strand	1012	1	5

Chain B: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	310-320	11
β-strand	325-328	4	6
α-helix	335-353	19
β-strand	359	1	6
β-strand	362-363	2	6
α-helix	366-372	7
α-helix	373-377	5
α-helix	378-381	4
β-strand	387-390	4	6
α-helix	400-406	7
β-strand	409-413	5	6
α-helix	414-420	7
α-helix	434-436	3
β-strand	439-442	4	6
α-helix	445-447	3
α-helix	453-472	20
β-strand	483-488	6	6
α-helix	499-513	15
α-helix	525-531	7
α-helix	534-535	2
β-strand	536-540	5	7
α-helix	550-565	16
α-helix	576-592	17
α-helix	598-616	19
α-helix	619-637	19
α-helix	671-691	21
α-helix	700-714	15
β-strand	721-724	4	7
α-helix	728-739	12
β-strand	751-753	3	7
α-helix	765-767	3
α-helix	768-780	13
β-strand	787-790	4	7
β-strand	805-807	3	7
α-helix	813-820	8
β-strand	829-833	5	7
α-helix	840-860	21
α-helix	866-886	21
β-strand	904	1	8
β-strand	905	1	9
β-strand	916	1	8
α-helix	917-919	3
β-strand	921-923	3	10
β-strand	927-929	3	10
α-helix	933-938	6
β-strand	940-941	2	10
β-strand	959-961	3	10
β-strand	967-971	5	10
β-strand	980-982	3	10
α-helix	984-986	3
β-strand	988-990	3	9
α-helix	991	1
β-strand	997-999	3	9
α-helix	1003-1005	3
β-strand	1012	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interferon-induced helicase C domain-containing protein 1	A, B	protein	699	Homo sapiens	Q9BYX4 (AlphaFold model)
RNA (5'-r(apupcpcpgpcpgpgpcpcpcpu)-3')	C, E	RNA	12
RNA (5'-r(papgpgpgpcpcpgpcpgpgpapu)-3')	D, F	RNA	12

Sequence of entity 1 (A, B), FASTA

>4GL2_1 Interferon-induced helicase C domain-containing protein 1 (chains A, B)
GPGAMLQLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVI
VLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENS
LLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIP
LPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFA
IADATREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVC
AEHLRKYNEALQINDTIRMIDAYTHLETFYNEEKDKKFAVIEDDLKKPLKLDETDRFLMT
LFFENNKMLKRLAENPEYENEKLTKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWI
TENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDI
KECNIVIRYGLVTNEIAMVQARGRARADESTYVLVAHSGSGVIERETVNDFREKMMYKAI
HCVQNMKPEEYAHKILELQMQSIMEKKMKTKRNIAKHYKNNPSLITFLCKNCSVLACSGE
DIHVIEKMHHVNMTPEFKELYIVRENKTLQKKCADYQINGEIICKCGQAWGTMMVHKGLD
LPCLKIRNFVVVFKNNSTKKQYKKWVELPITFPNLDYSE

Sequence of entity 2 (C, E), FASTA

>4GL2_2 RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3') (chains C, E)
AUCCGCGGCCCU

Sequence of entity 3 (D, F), FASTA

>4GL2_3 RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3') (chains D, F)
AGGGCCGCGGAU

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

Primary citation

Structural Basis for dsRNA Recognition, Filament Formation, and Antiviral Signal Activation by MDA5. Wu, B., Peisley, A., Richards, C. et al. Cell (2013) 152:276-289. DOI 10.1016/j.cell.2012.11.048 · 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
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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