PDBsum entry 5jbg

Immune system

PDB id: 5jbg

Contents

Protein chain

661 a.a.

DNA/RNA

Ligands

ADP

ALF

SO4 ×5

Metals

_ZN

_MG

Waters ×268

PDB id:

5jbg

Name:

Immune system

Title:

Crystal structure of chicken lgp2 with 5'ppp 26-mer hairpin RNA with 3' gg overhang and adp-alf4-mg2+ at 2.0 a resolution.

Structure:

Lgp2. Chain: a. Engineered: yes. Mutation: yes. RNA (5'- r( Gppp Gp Ap Gp Cp Gp Up Gp Cp Cp Gp Gp Gp Cp Ap Cp Gp Cp Up Cp Cp G p G)-3'). Chain: x. Engineered: yes.

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: rosetta 2. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

2.00Å R-factor: 0.219 R-free: 0.255

Authors:

S.Cusack,E.Uchikawa

Key ref:

E.Uchikawa et al. (2016). Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5. Mol Cell, 62, 586-602. PubMed id: 27203181 DOI: 10.1016/j.molcel.2016.04.021

Date:

13-Apr-16 Release date: 01-Jun-16

Protein chain

G0YYQ5  (G0YYQ5_CHICK) -  RNA helicase from Gallus gallus

Seq: 674 a.a.

Struc: 661 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chain

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

Enzyme reactions

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

ATP + H2O = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + H(+)

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

reference

DOI no: 10.1016/j.molcel.2016.04.021

Mol Cell 62:586-602 (2016)

PubMed id: 27203181

Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5.

E.Uchikawa, M.Lethier, H.Malet, J.Brunel, D.Gerlier, S.Cusack.

ABSTRACT

RIG-I and MDA5 sense virus-derived short 5'ppp blunt-ended or long dsRNA, respectively, causing interferon production. Non-signaling LGP2 appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. Co-crystal structures of chicken (ch) LGP2 with dsRNA display a fully or semi-closed conformation depending on the presence or absence of nucleotide. LGP2 caps blunt, 3' or 5' overhang dsRNA ends with 1 bp longer overall footprint than RIG-I. Structures of 1:1 and 2:1 complexes of chMDA5 with short dsRNA reveal head-to-head packing rather than the polar head-to-tail orientation described for long filaments. chLGP2 and chMDA5 make filaments with a similar axial repeat, although less co-operatively for chLGP2. Overall, LGP2 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. Functionally, RNA binding is required for LGP2-mediated enhancement of MDA5 activation. We propose that LGP2 end-binding may promote nucleation of MDA5 oligomerization on dsRNA.