4QGU

protein domain complex with ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

New insights into the structural basis of DNA recognition by HINa and HINb domains of IFI16.

Ni, X.Ru, H.Ma, F.Zhao, L.Shaw, N.Feng, Y.Ding, W.Gong, W.Wang, Q.Ouyang, S.Cheng, G.Liu, Z.J.

(2016) J Mol Cell Biol 8: 51-61

  • DOI: 10.1093/jmcb/mjv053
  • Primary Citation of Related Structures:  
    4QGU

  • PubMed Abstract: 
  • Interferon gamma-inducible protein 16 (IFI16) senses DNA in the cytoplasm and the nucleus by using two tandem hematopoietic interferon-inducible nuclear (HIN) domains, HINa and HINb, through the cooperative assembly of IFI16 filaments on double-stranded DNA (dsDNA) ...

    Interferon gamma-inducible protein 16 (IFI16) senses DNA in the cytoplasm and the nucleus by using two tandem hematopoietic interferon-inducible nuclear (HIN) domains, HINa and HINb, through the cooperative assembly of IFI16 filaments on double-stranded DNA (dsDNA). The role of HINa in sensing DNA is not clearly understood. Here, we describe the crystal structure of the HINa domain in complex with DNA at 2.55 Å resolution and provide the first insight into the mode of DNA binding by the HINa domain. The structure reveals the presence of two oligosaccharide/nucleotide-binding (OB) folds with a unique DNA-binding surface. HINa uses loop L45 of the canonical OB2 fold to bind to the DNA backbone. The dsDNA is recognized as two single strands of DNA. Interestingly, deletion of HINb compromises the ability of IFI16 to induce IFN-β, while HINa mutants impaired in DNA binding enhance the production of IFN-β. These results shed light on the roles of IFI16 HIN domains in DNA recognition and innate immune responses.


    Organizational Affiliation

    Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, China National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China iHuman Institute, ShanghaiTech University, Shanghai 201210, China zjliu@ibp.ac.cn gcheng@mednet.ucla.edu ouyangsy@moon.ibp.ac.cn.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-interferon-inducible protein 16A, B206Homo sapiensMutation(s): 0 
Gene Names: IFI16IFNGIP1
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
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*GP*GP*CP*CP*GP*GP*CP*GP*TP*GP*A)-3')C, D12N/A
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.715α = 90
b = 91.865β = 90
c = 69.978γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references