SMTL ID : 5f9f.1

Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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.6: 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.12: 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.16: 5 residues within 4Å: Chain G: C.580, C.583, C.634, C.639, H.641 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.580, G:C.583, G:C.634, G:C.639 ZN.22: 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.26: 4 residues within 4Å: Chain K: C.580, C.583, C.634, C.639 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)(Non-functional Binders)

MG.2: 1 residues within 4Å: Chain A: K.493 No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain G: S.468 No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain I: K.493 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain K: S.468, K.493 No protein-ligand interaction detected (PLIP)

4 x ETF: TRIFLUOROETHANOL(Non-covalent)

ETF.3: 9 residues within 4Å: Chain A: I.32, C.33, A.34, C.38, K.40, L.178, T.179, A.180, E.472 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.472 ETF.13: 5 residues within 4Å: Chain E: K.436, N.438, Q.439, D.642, K.658 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.438, E:N.438 Halogen bonds: E:D.642 ETF.17: 9 residues within 4Å: Chain G: R.90, Q.106, I.107, N.110, N.111 Chain K: Q.106, I.107, N.110, N.111 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.90, G:N.111 ETF.28: 6 residues within 4Å: Chain K: P.226, K.228, M.494, T.497, R.498, C.508 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:T.497

13 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.4: 8 residues within 4Å: Chain A: E.280, R.316, D.320, I.324, Y.336, T.406, A.408 Chain B: A.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.324, A:T.406, A:A.408 Hydrogen bonds: A:D.320 BU3.5: 5 residues within 4Å: Chain A: G.39, K.40, T.41, F.42, D.475 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.42 Hydrogen bonds: A:D.475 BU3.8: 4 residues within 4Å: Chain C: K.436, T.437, N.438, K.658 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:K.436, C:N.438 Hydrogen bonds: C:T.437, C:N.438, C:N.438, C:K.658 BU3.9: 9 residues within 4Å: Chain A: R.90, Q.106, I.107, N.110, N.111 Chain C: R.90, I.107, N.110, N.111 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.107, C:N.110, A:I.107 Hydrogen bonds: C:R.90, C:N.111, A:N.110 BU3.10: 6 residues within 4Å: Chain C: N.146, H.151, A.470, D.471 Chain D: A.5, U.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.151 BU3.11: 8 residues within 4Å: Chain C: L.20, I.32, A.34, P.35, C.38, K.40, L.178, T.179 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.20, C:I.32, C:A.34, C:K.40, C:K.40 Hydrogen bonds: C:A.34 BU3.14: 8 residues within 4Å: Chain E: L.20, I.32, A.34, C.38, K.40, V.43, L.178, T.179 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.32, E:K.40, E:V.43, E:L.178 BU3.15: 9 residues within 4Å: Chain E: L.484, Y.487, G.489, N.490, K.493, M.494, T.497, E.521, N.524 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.484, E:Y.487, E:M.494, E:T.497 Hydrogen bonds: E:N.490, E:E.521 Water bridges: E:K.228 BU3.18: 7 residues within 4Å: Chain G: I.32, A.34, P.35, C.38, K.40, T.179, E.472 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:A.34, G:K.40, G:K.40 Hydrogen bonds: G:I.32, G:A.34, G:T.179 BU3.19: 6 residues within 4Å: Chain G: A.99, E.100, I.120, N.123, N.124 Chain H: C.24 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:I.120, G:N.123 Hydrogen bonds: G:A.99, G:E.100 BU3.20: 7 residues within 4Å: Chain G: L.484, Y.487, V.488, G.489, K.493, T.497, E.521 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:Y.487, G:K.493 Hydrogen bonds: G:T.497, G:T.497 BU3.25: 8 residues within 4Å: Chain I: I.32, C.33, A.34, P.35, C.38, K.40, L.178, T.179 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:I.32, I:K.40, I:L.178 Hydrogen bonds: I:A.34 BU3.29: 8 residues within 4Å: Chain K: I.32, A.34, C.38, G.39, K.40, V.43, L.178, T.179 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:I.32, K:A.34, K:K.40, K:V.43, K:L.178 Hydrogen bonds: K:T.179

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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