8JKL

IRF4 DNA-binding domain bound to an DNA containing GATA motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency.

Wang, G.Feng, X.Ding, J.

(2023) Structure 31: 1441

  • DOI: https://doi.org/10.1016/j.str.2023.08.013
  • Primary Citation of Related Structures:  
    8JKL, 8JKN, 8JKO, 8JKQ, 8JKS

  • PubMed Abstract: 

    Interferon regulatory factor 4 (IRF4) is a transcription factor that regulates the development and function of immune cells. Recently, a new multimorphic mutation T95R was identified in the IRF4 DNA-binding domain (DBD) in patients with autosomal dominant combined immune deficiency. Here, we characterized the interactions of the wild-type IRF4-DBD (IRF4-DBD WT ) and T95R mutant (IRF4-DBD T95R ) with a canonical DNA sequence and several noncanonical DNA sequences. We found that compared to IRF4-DBD WT , IRF4-DBD T95R exhibits higher binding affinities for both canonical and noncanonical DNAs, with the highest preference for the noncanonical GATA sequence. The crystal structures of IRF4-DBD WT in complex with the GATA sequence and IRF4-DBD T95R in complexes with both canonical and noncanonical DNAs were determined, showing that the T95R mutation enhances the interactions of IRF4-DBD T95R with the canonical and noncanonical DNAs to achieve higher affinity and specificity. Collectively, our data provide the molecular basis for the gain-of-function and new function of IRF4 T95R .


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon regulatory factor 4E [auth G],
F [auth C],
G [auth D],
H
116Homo sapiensMutation(s): 0 
Gene Names: IRF4hCG_20902
UniProt & NIH Common Fund Data Resources
Find proteins for F2Z3D5 (Homo sapiens)
Explore F2Z3D5 
Go to UniProtKB:  F2Z3D5
GTEx:  ENSG00000137265 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z3D5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
GATA-ForwardA,
C [auth E]
19Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
GATA-ReverseB,
D [auth F]
19Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.56α = 90
b = 117.56β = 90
c = 150.51γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB37030305

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Database references