SMTL ID : 9f2l.1

Cryo-EM structure of the I923V MDA5-dsRNA filament with ADP-AlF4 bound and 73-degree helical twist

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: C.910, N.912, C.913, C.965, C.967, Q.969, W.971 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.910, A:C.913, A:C.965, A:C.967 ZN.4: 7 residues within 4Å: Chain D: C.910, N.912, C.913, C.965, C.967, Q.969, W.971 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.910, D:C.913, D:C.965, D:C.967

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 13 residues within 4Å: Chain A: Q.329, L.330, R.331, Q.334, T.353, G.354, S.355, G.356, K.357, T.358, R.359, R.827 Ligands: ALF.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.329, A:R.331, A:R.331, A:G.354, A:S.355, A:G.356, A:K.357, A:T.358, A:T.358, A:R.359 Salt bridges: A:K.357 pi-Cation interactions: A:R.331 ADP.5: 13 residues within 4Å: Chain D: Q.329, L.330, R.331, Q.334, T.353, G.354, S.355, G.356, K.357, T.358, R.359, R.827 Ligands: ALF.6 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Q.329, D:R.331, D:R.331, D:G.354, D:S.355, D:G.356, D:K.357, D:T.358, D:T.358, D:R.359 Salt bridges: D:K.357 pi-Cation interactions: D:R.331

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.3: 6 residues within 4Å: Chain A: T.353, G.354, K.357, A.511, R.825 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) ALF.6: 6 residues within 4Å: Chain D: T.353, G.354, K.357, A.511, R.825 Ligands: ADP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R. et al., Molecular basis of autoimmune disease protection by MDA5 variants. Biorxiv (2024)

Release Date

2025-02-26

Peptides

Interferon-induced helicase C domain-containing protein 1: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

Interferon-induced helicase C domain-containing protein 1

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