SMTL ID : 5f98.1

Crystal structure of RIG-I in complex with Cap-0 RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.28 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.580, A:C.583, A:C.634, A:C.639 ZN.4: 4 residues within 4Å: Chain C: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.580, C:C.583, C:C.634, C:C.639 ZN.7: 4 residues within 4Å: Chain E: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.580, E:C.583, E:C.634, E:C.639 ZN.10: 4 residues within 4Å: Chain G: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.580, G:C.583, G:C.634, G:C.639 ZN.13: 4 residues within 4Å: Chain I: C.580, C.583, C.634, C.639 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.580, I:C.583, I:C.634, I:C.639 ZN.16: 5 residues within 4Å: Chain K: C.580, C.583, C.634, C.639, W.643 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.580, K:C.583, K:C.634, K:C.639

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: H.600, S.624 Chain B: G.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.600 MG.5: 3 residues within 4Å: Chain C: E.597, H.600, S.624 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain E: E.597, H.600 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain G: E.597, H.600, S.624 Chain H: G.1 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain I: E.597, H.600, S.624 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain K: C.599, H.600 Chain L: G.1 No protein-ligand interaction detected (PLIP)

6 x M7G: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE(Non-covalent)

M7G.3: 8 residues within 4Å: Chain A: H.617, K.621, K.628, K.631, D.642, I.645, K.658 Chain B: G.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.631, A:K.631, A:K.658 Salt bridges: A:H.617, A:K.621, A:K.628, A:K.628, A:K.631 M7G.6: 8 residues within 4Å: Chain C: H.617, P.618, K.621, K.628, K.631, I.645, K.658 Chain D: G.1 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.658, C:K.658 Salt bridges: C:H.617, C:K.621, C:K.628, C:K.628, C:K.631 M7G.9: 6 residues within 4Å: Chain E: H.617, K.628, K.631, D.642, I.645 Chain F: G.1 4 PLIP interactions: 4 interactions with chain E Salt bridges: E:H.617, E:K.628, E:K.628, E:K.631 M7G.12: 6 residues within 4Å: Chain G: H.617, K.628, K.631, I.645, K.658 Chain H: G.1 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:K.658, G:K.658 Salt bridges: G:H.617, G:K.628, G:K.628, G:K.631 M7G.15: 6 residues within 4Å: Chain I: H.617, K.628, K.631, D.642, I.645 Chain J: G.1 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:K.631, I:D.642 Salt bridges: I:H.617, I:K.621, I:K.628, I:K.628, I:K.631 M7G.18: 6 residues within 4Å: Chain K: H.617, K.628, K.631, D.642, I.645 Chain L: G.1 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:D.642 Salt bridges: K:H.617, K:K.628, K:K.628, K:K.631

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Devarkar, S.C. et al., Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-01-13

Peptides

Probable ATP-dependent RNA helicase DDX58: ACEGIK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

Probable ATP-dependent RNA helicase DDX58

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