8HCM

zebrafish IRF-11 DBD complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.236 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of DNA-bound Fish IRF10 and IRF11 Reveal the Determinants of IFN Regulation.

Wang, Z.X.Liu, B.Xie, H.Liu, X.Li, X.Shi, F.Ouyang, S.Zhang, Y.A.

(2024) J Immunol 213: 743-752

  • DOI: https://doi.org/10.4049/jimmunol.2300414
  • Primary Citation of Related Structures:  
    8HCL, 8HCM, 8HCS

  • PubMed Abstract: 

    IFN regulatory factors (IRFs) are transcription factors that mediate homeostatic mechanisms of host defense against pathogens. In addition to IRF1-9, which are conserved across vertebrates, teleost fishes have two other IRFs, IRF10 and IRF11. In zebrafish (Danio rerio), IRF10 represses the expression of IFNφ1 and IFNφ3, whereas IRF11 exerts the opposite effect. In this study, we found IRF10 could significantly inhibit the expression of IFNφ1 and IFNφ3 induced by IFN11 to synergistically regulate type I IFN expression. To clarify the synergistically regulatory mechanism of IRF10 and IRF11 in type I IFN expression, we determined and analyzed the crystal structures of the DNA-binding domains (DBDs) of zebrafish IRF10 and IRF11 bound to DNA, as well as IRF11 DBD in apo form. The interactions of IRF10-DBD and IRF11-DBD with DNA backbone were elaborated in detail. Further analysis showed that IRF10 and IRF11 have the same binding patterns and comparable affinities with the IFN-sensitive response elements of IFNφ1 and IFNφ3 promoters. Therefore, IRF10 could function as a controlling factor for IRF11 by competitive binding of the IFN-sensitive response elements to coregulate the host IFN response. Accordingly, similar to IRF1 and IRF2 in mammals, IRF10 and IRF11 act as another pair of negative and positive regulators to balance the antiviral responses in fish.


  • Organizational Affiliation

    State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon regulatory factor108Danio rerioMutation(s): 0 
Gene Names: irf1
UniProt
Find proteins for Q1RLP9 (Danio rerio)
Explore Q1RLP9 
Go to UniProtKB:  Q1RLP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1RLP9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*AP*GP*AP*AP*AP*GP*TP*GP*AP*AP*AP*GP*C)-3')14synthetic construct
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*CP*TP*TP*TP*CP*AP*CP*TP*TP*TP*CP*TP*A)-3')14synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.236 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.118α = 90
b = 61.118β = 90
c = 220.054γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31725026; 82225028; 82172287

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Database references
  • Version 1.2: 2024-09-04
    Changes: Database references