5Z7D

p204HINab-dsDNA complex structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural mechanism of DNA recognition by the p204 HIN domain.

Fan, X.Jiang, J.Zhao, D.Chen, F.Ma, H.Smith, P.Unterholzner, L.Xiao, T.S.Jin, T.

(2021) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkab076
  • Primary Citation of Related Structures:  
    5YZP, 5YZW, 5Z7D

  • PubMed Abstract: 
  • The interferon gamma-inducible protein 16 (IFI16) and its murine homologous protein p204 function in non-sequence specific dsDNA sensing; however, the exact dsDNA recognition mechanisms of IFI16/p204, which harbour two HIN domains, remain unclear. In the present study, we determined crystal structures of p204 HINa and HINb domains, which are highly similar to those of other PYHIN family proteins ...

    The interferon gamma-inducible protein 16 (IFI16) and its murine homologous protein p204 function in non-sequence specific dsDNA sensing; however, the exact dsDNA recognition mechanisms of IFI16/p204, which harbour two HIN domains, remain unclear. In the present study, we determined crystal structures of p204 HINa and HINb domains, which are highly similar to those of other PYHIN family proteins. Moreover, we obtained the crystal structure of p204 HINab domain in complex with dsDNA and provided insights into the dsDNA binding mode. p204 HINab binds dsDNA mainly through α2 helix of HINa and HINb, and the linker between them, revealing a similar HIN:DNA binding mode. Both HINa and HINb are vital for HINab recognition of dsDNA, as confirmed by fluorescence polarization assays. Furthermore, a HINa dimerization interface was observed in structures of p204 HINa and HINab:dsDNA complex, which is involved in binding dsDNA. The linker between HINa and HINb reveals dynamic flexibility in solution and changes its direction at ∼90° angle in comparison with crystal structure of HINab:dsDNA complex. These structural information provide insights into the mechanism of DNA recognition by different HIN domains, and shed light on the unique roles of two HIN domains in activating the IFI16/p204 signaling pathway.


    Organizational Affiliation

    CAS Center for Excellence in Molecular Cell Science, Shanghai, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon-activable protein 204A, B, C412Mus musculusMutation(s): 0 
Gene Names: Ifi204
UniProt & NIH Common Fund Data Resources
Find proteins for P0DOV2 (Mus musculus)
Explore P0DOV2 
Go to UniProtKB:  P0DOV2
IMPC:  MGI:96429
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*CP*AP*TP*CP*AP*GP*AP*AP*AP*GP*AP*GP*AP*GP*C)-3')D [auth I], F [auth K]16Vaccinia virus
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*CP*AP*TP*CP*AP*GP*AP*AP*AP*GP*AP*GP*AP*GP*C)-3')E [auth J], G [auth L]16Vaccinia virus
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.39α = 90
b = 101.39β = 90
c = 783.61γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 2.0: 2021-03-10
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary