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 

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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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon regulatory factor 3C [auth A],
D [auth B]		112Homo sapiensMutation(s): 0 
Gene Names: IRF3
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PHAROS:  Q14653
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UniProt GroupQ14653
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor AP-1E [auth C]62Homo sapiensMutation(s): 1 
Gene Names: JUN
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Find proteins for P05412 (Homo sapiens)
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PHAROS:  P05412
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UniProt GroupP05412
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclic-AMP-dependent transcription factor ATF-2F [auth D]61Homo sapiensMutation(s): 1 
Gene Names: ATF2, CREB2, CREBP1
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Find proteins for P15336 (Homo sapiens)
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PHAROS:  P15336
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UniProt GroupP15336
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Entity ID: 1
MoleculeChainsLengthOrganismImage
31-MERA [auth E]31N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
31-MERB [auth F]31N/A
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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