PDBsum entry 5f9h

Hydrolase/RNA

PDB id: 5f9h

Contents

Protein chains

(+ 0 more) 646 a.a.

DNA/RNA

Ligands

GTP ×6

Metals

_MG ×8

_ZN ×6

PDB id:

5f9h

Name:

Hydrolase/RNA

Title:

Crystal structure of rig-i helicase-rd in complex with 24-mer 5' triphosphate hairpin RNA

Structure:

Probable atp-dependent RNA helicase ddx58. Chain: a, c, e, g, i, k. Synonym: dead box protein 58,rig-i-like receptor 1,rlr-1,retinoic acid-inducible gene 1 protein,rig-1,retinoic acid-inducible gene i protein,rig-i. Engineered: yes. RNA (5'- r(p Ap Ap Up Ap Up Ap Ap Up Ap Gp Up Gp Ap Up Ap Up Up Ap Up Ap Up Up C)-3').

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ddx58. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

3.10Å R-factor: 0.216 R-free: 0.266

Authors:

C.Wang,J.Marcotrigiano,M.Miller,F.Jiang

Key ref:

S.C.Devarkar et al. (2016). Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proc Natl Acad Sci U S A, 113, 596-601. PubMed id: 26733676 DOI: 10.1073/pnas.1515152113

Date:

09-Dec-15 Release date: 13-Jan-16

Protein chains

O95786  (DDX58_HUMAN) -  Antiviral innate immune response receptor RIG-I from Homo sapiens

Seq: 925 a.a.

Struc: 646 a.a.

DNA/RNA chains

A-A-U-A-U-A-A-U-A-G-U-G-A-U-A-U-U-A-U-A-U-U-C 23 bases

A-A-U-A-U-A-A-U-A-G-U-G-A-U-A-U-U-A-U-A-U-U-C 23 bases

A-A-U-A-U-A-A-U-A-G-U-G-A-U-A-U-U-A-U-A-U-U-C 23 bases

A-A-U-A-U-A-A-U-A-G-U-G-A-U-A-U-U-A-U-A-U-U-C 23 bases

A-A-U-A-U-A-A-U-A-G-U-G-A-U-A-U-U-A-U-A-U-U-C 23 bases

A-A-U-A-U-A-A-U-A-G-U-G-A-U-A-U-U-A-U-A-U-U-C 23 bases

Enzyme reactions

• Enzyme class: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP (Bound ligand (Het Group name = GTP) matches with 96.88% similarity) + H2O = ADP + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1515152113

Proc Natl Acad Sci U S A 113:596-601 (2016)

PubMed id: 26733676

Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I.

S.C.Devarkar, C.Wang, M.T.Miller, A.Ramanathan, F.Jiang, A.G.Khan, S.S.Patel, J.Marcotrigiano.

ABSTRACT

RNAs with 5'-triphosphate (ppp) are detected in the cytoplasm principally by the innate immune receptor Retinoic Acid Inducible Gene-I (RIG-I), whose activation triggers a Type I IFN response. It is thought that self RNAs like mRNAs are not recognized by RIG-I because 5'ppp is capped by the addition of a 7-methyl guanosine (m7G) (Cap-0) and a 2'-O-methyl (2'-OMe) group to the 5'-end nucleotide ribose (Cap-1). Here we provide structural and mechanistic basis for exact roles of capping and 2'-O-methylation in evading RIG-I recognition. Surprisingly, Cap-0 and 5'ppp double-stranded (ds) RNAs bind to RIG-I with nearly identical Kd values and activate RIG-I's ATPase and cellular signaling response to similar extents. On the other hand, Cap-0 and 5'ppp single-stranded RNAs did not bind RIG-I and are signaling inactive. Three crystal structures of RIG-I complexes with dsRNAs bearing 5'OH, 5'ppp, and Cap-0 show that RIG-I can accommodate the m7G cap in a cavity created through conformational changes in the helicase-motif IVa without perturbing the ppp interactions. In contrast, Cap-1 modifications abrogate RIG-I signaling through a mechanism involving the H830 residue, which we show is crucial for discriminating between Cap-0 and Cap-1 RNAs. Furthermore, m7G capping works synergistically with 2'-O-methylation to weaken RNA affinity by 200-fold and lower ATPase activity. Interestingly, a single H830A mutation restores both high-affinity binding and signaling activity with 2'-O-methylated dsRNAs. Our work provides new structural insights into the mechanisms of host and viral immune evasion from RIG-I, explaining the complexity of cap structures over evolution.