3RNU

Structural Basis of Cytosolic DNA Sensing by Innate Immune Receptors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.502 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor.

Jin, T., Perry, A., Jiang, J., Smith, P., Curry, J.A., Unterholzner, L., Jiang, Z., Horvath, G., Rathinam, V.A., Johnstone, R.W., Hornung, V., Latz, E., Bowie, A.G., Fitzgerald, K.A., Xiao, T.S.

(2012) Immunity 36: 561-571

  • DOI: 10.1016/j.immuni.2012.02.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Recognition of DNA by the innate immune system is central to antiviral and antibacterial defenses, as well as an important contributor to autoimmune diseases involving self DNA. AIM2 (absent in melanoma 2) and IFI16 (interferon-inducible protein 16) ...

    Recognition of DNA by the innate immune system is central to antiviral and antibacterial defenses, as well as an important contributor to autoimmune diseases involving self DNA. AIM2 (absent in melanoma 2) and IFI16 (interferon-inducible protein 16) have been identified as DNA receptors that induce inflammasome formation and interferon production, respectively. Here we present the crystal structures of their HIN domains in complex with double-stranded (ds) DNA. Non-sequence-specific DNA recognition is accomplished through electrostatic attraction between the positively charged HIN domain residues and the dsDNA sugar-phosphate backbone. An intramolecular complex of the AIM2 Pyrin and HIN domains in an autoinhibited state is liberated by DNA binding, which may facilitate the assembly of inflammasomes along the DNA staircase. These findings provide mechanistic insights into dsDNA as the activation trigger and oligomerization platform for the assembly of large innate signaling complexes such as the inflammasomes.

    Organizational Affiliation: 

    Structural Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-0430, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-interferon-inducible protein 16
A, B, C, D
204Homo sapiensMutation(s): 0 
Gene Names: IFI16 (IFNGIP1)
Find proteins for Q16666 (Homo sapiens)
Go to Gene View: IFI16
Go to UniProtKB:  Q16666
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3')K16N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*GP*GP*CP*C)-3')L16N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT
Download SDF File 
Download CCD File 
A, B, C, D
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
B, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.502 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 126.841α = 90.00
b = 126.841β = 90.00
c = 163.868γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-04-22 
  • Released Date: 2012-04-25 
  • Deposition Author(s): Jin, T.C., Xiao, T.

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-09
    Type: Database references
  • Version 1.2: 2015-01-28
    Type: Other