7O56

X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an interferon-stimulated response element solved by Phosphorus and Sulphur SAD methods


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4.

Agnarelli, A.El Omari, K.Duman, R.Wagner, A.Mancini, E.J.

(2021) Acta Crystallogr F Struct Biol Commun 77: 202-207

  • DOI: https://doi.org/10.1107/S2053230X21006506
  • Primary Citation of Related Structures:  
    7O56

  • PubMed Abstract: 

    Pivotal to the regulation of key cellular processes such as the transcription, replication and repair of DNA, DNA-binding proteins play vital roles in all aspects of genetic activity. The determination of high-quality structures of DNA-binding proteins, particularly those in complexes with DNA, provides crucial insights into the understanding of these processes. The presence in such complexes of phosphate-rich oligonucleotides offers the choice of a rapid method for the routine solution of DNA-binding proteins through the use of long-wavelength beamlines such as I23 at Diamond Light Source. This article reports the use of native intrinsic phosphorus and sulfur single-wavelength anomalous dispersion methods to solve the complex of the DNA-binding domain (DBD) of interferon regulatory factor 4 (IRF4) bound to its interferon-stimulated response element (ISRE). The structure unexpectedly shows three molecules of the IRF4 DBD bound to one ISRE. The sole reliance on native intrinsic anomalous scattering elements that belong to DNA-protein complexes renders the method of general applicability to a large number of such protein complexes that cannot be solved by molecular replacement or by other phasing methods.


  • Organizational Affiliation

    School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, United Kingdom.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon regulatory factor 4A,
D [auth B],
E [auth C]
141Homo sapiensMutation(s): 0 
Gene Names: IRF4MUM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15306 (Homo sapiens)
Explore Q15306 
Go to UniProtKB:  Q15306
PHAROS:  Q15306
GTEx:  ENSG00000137265 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15306
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*AP*TP*AP*AP*AP*AP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*A)-3')B [auth D]21synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*TP*TP*TP*TP*AP*T)-3')C [auth E]21synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.88α = 90
b = 112.44β = 90
c = 140.66γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom204833/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection