1T2K

Structure Of The DNA Binding Domains Of IRF3, ATF-2 and Jun Bound To DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-beta enhancer.

Panne, D.Maniatis, T.Harrison, S.C.

(2004) EMBO J 23: 4384-4393

  • DOI: https://doi.org/10.1038/sj.emboj.7600453
  • Primary Citation of Related Structures:  
    1T2K

  • PubMed Abstract: 

    Transcriptional activation of the interferon-beta (IFN-beta) gene requires assembly of an enhanceosome containing the transcription factors ATF-2/c-Jun, IRF-3/IRF-7, NF-kappaB and HMGI(Y). These factors cooperatively bind a composite DNA site and activate expression of the IFN-beta gene. The 3.0 A crystal structure of the DNA-binding domains of ATF-2/c-Jun and two IRF-3 molecules in a complex with 31 base pairs (bp) of the PRDIV-PRDIII region of the IFN-beta enhancer shows that association of the four proteins with DNA creates a continuous surface for the recognition of 24 bp. The structure, together with in vitro binding studies and protein mutagenesis, shows that protein-protein interactions are not critical for cooperative binding. Instead, cooperativity arises mainly through nucleotide sequence-dependent structural changes in the DNA that allow formation of complementary DNA conformations. Because the binding sites overlap on the enhancer, the unit of recognition is the entire nucleotide sequence, not the individual subsites.


  • Organizational Affiliation

    Department of Biological Chemistry & Molecular Pharmacology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon regulatory factor 3C [auth A],
D [auth B]
112Homo sapiensMutation(s): 0 
Gene Names: IRF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q14653 (Homo sapiens)
Explore Q14653 
Go to UniProtKB:  Q14653
PHAROS:  Q14653
GTEx:  ENSG00000126456 
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UniProt GroupQ14653
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor AP-1E [auth C]62Homo sapiensMutation(s): 1 
Gene Names: JUN
UniProt & NIH Common Fund Data Resources
Find proteins for P05412 (Homo sapiens)
Explore P05412 
Go to UniProtKB:  P05412
PHAROS:  P05412
GTEx:  ENSG00000177606 
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UniProt GroupP05412
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic-AMP-dependent transcription factor ATF-2F [auth D]61Homo sapiensMutation(s): 1 
Gene Names: ATF2CREB2CREBP1
UniProt & NIH Common Fund Data Resources
Find proteins for P15336 (Homo sapiens)
Explore P15336 
Go to UniProtKB:  P15336
PHAROS:  P15336
GTEx:  ENSG00000115966 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15336
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
31-MERA [auth E]31N/A
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Entity ID: 2
MoleculeChains LengthOrganismImage
31-MERB [auth F]31N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.38α = 90
b = 65.21β = 93.44
c = 83.85γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description