5JBJ | pdb_00005jbj

Crystal structure of chicken LGP2 with 5'p 12-mer dsRNA at 3.6 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 
    0.319 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.256 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5JBJ

This is version 1.1 of the entry. See complete history

Literature

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

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

(2016) Mol Cell 62: 586-602

  • DOI: https://doi.org/10.1016/j.molcel.2016.04.021
  • Primary Citation Related Structures: 
    5JAJ, 5JB2, 5JBG, 5JBJ, 5JC3, 5JC7, 5JCF, 5JCH

  • PubMed 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.


  • Organizational Affiliation
    • European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; University Grenoble Alpes, Centre National de la Recherche Scientifique, EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.

Macromolecule Content 

  • Total Structure Weight: 85.18 kDa 
  • Atom Count: 5,540 
  • Modeled Residue Count: 651 
  • Deposited Residue Count: 704 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LGP2680Gallus gallusMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for G0YYQ5 (Gallus gallus)
Explore G0YYQ5 
Go to UniProtKB:  G0YYQ5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0YYQ5
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')B [auth X],
C [auth Y]
12synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free:  0.319 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.256 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.09α = 90
b = 90.09β = 90
c = 196.73γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFrance322586

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description