3RNU

Structural Basis of Cytosolic DNA Sensing by Innate Immune Receptors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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:  
    3RLN, 3RLO, 3RN2, 3RN5, 3RNU

  • 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) have been identified as DNA receptors that induce inflammasome formation and interferon production, respectively ...

    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

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-interferon-inducible protein 16A, B, C, D204Homo sapiensMutation(s): 0 
Gene Names: IFI16, IFNGIP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16666 (Homo sapiens)
Explore Q16666 
Go to UniProtKB:  Q16666
PHAROS:  Q16666
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16666
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3')E [auth K]16N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*GP*GP*CP*C)-3')F [auth L]16N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.841α = 90
b = 126.841β = 90
c = 163.868γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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