PDBsum entry 4bpb

Hydrolase/RNA

PDB id: 4bpb

Contents

Protein chain

634 a.a.

DNA/RNA

Ligands

SO4

Metals

_ZN

Waters ×107

PDB id:

4bpb

Name:

Hydrolase/RNA

Title:

Structural insights into RNA recognition by rig-i

Structure:

Probable atp-dependent RNA helicase ddx58. Chain: a. Fragment: residues 230-925. Synonym: dead box protein 58, retinoic acid-inducible gene 1 protein, rig-1, retinoic acid-inducible gene i protein, rig-i. Engineered: yes. 5'-r( Gp Cp Gp Cp Gp Cp Gp Cp Gp Cp)-3'. Chain: c, d

Source:

Homo sapiens. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Organism_taxid: 9606

Resolution:

2.58Å R-factor: 0.198 R-free: 0.255

Authors:

D.Luo,A.M.Pyle

Key ref:

D.Luo et al. (2011). Structural insights into RNA recognition by RIG-I. Cell, 147, 409-422. PubMed id: 22000018

Date:

23-May-13 Release date: 19-Jun-13

Protein chain

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

Seq: 925 a.a.

Struc: 634 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

G-C-G-C-G-C-G-C-G-C 10 bases

G-C-G-C-G-C-G-C-G-C 10 bases

Enzyme reactions

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

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

reference

Cell 147:409-422 (2011)

PubMed id: 22000018

Structural insights into RNA recognition by RIG-I.

D.Luo, S.C.Ding, A.Vela, A.Kohlway, B.D.Lindenbach, A.M.Pyle.

ABSTRACT

Intracellular RIG-I-like receptors (RLRs, including RIG-I, MDA-5, and LGP2) recognize viral RNAs as pathogen-associated molecular patterns (PAMPs) and initiate an antiviral immune response. To understand the molecular basis of this process, we determined the crystal structure of RIG-I in complex with double-stranded RNA (dsRNA). The dsRNA is sheathed within a network of protein domains that include a conserved "helicase" domain (regions HEL1 and HEL2), a specialized insertion domain (HEL2i), and a C-terminal regulatory domain (CTD). A V-shaped pincer connects HEL2 and the CTD by gripping an α-helical shaft that extends from HEL1. In this way, the pincer coordinates functions of all the domains and couples RNA binding with ATP hydrolysis. RIG-I falls within the Dicer-RIG-I clade of the superfamily 2 helicases, and this structure reveals complex interplay between motor domains, accessory mechanical domains, and RNA that has implications for understanding the nanomechanical function of this protein family and other ATPases more broadly.