2O61

Crystal Structure of NFkB, IRF7, IRF3 bound to the interferon-b enhancer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


Literature

An Atomic Model of the Interferon-beta Enhanceosome.

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

(2007) Cell 129: 1111-1123

  • DOI: 10.1016/j.cell.2007.05.019
  • Primary Citation of Related Structures:  
    2O61, 2O6G

  • PubMed Abstract: 

    • Transcriptional activation of the interferon-beta (IFN-beta) gene requires assembly of an enhanceosome containing ATF-2/c-Jun, IRF-3/IRF-7, and NFkappaB. These factors bind cooperatively to the IFN-beta enhancer and recruit coactivators and chromatin-remodeling proteins to the IFN-beta promoter ...

    Transcriptional activation of the interferon-beta (IFN-beta) gene requires assembly of an enhanceosome containing ATF-2/c-Jun, IRF-3/IRF-7, and NFkappaB. These factors bind cooperatively to the IFN-beta enhancer and recruit coactivators and chromatin-remodeling proteins to the IFN-beta promoter. We describe here a crystal structure of the DNA-binding domains of IRF-3, IRF-7, and NFkappaB, bound to one half of the enhancer, and use a previously described structure of the remaining half to assemble a complete picture of enhanceosome architecture in the vicinity of the DNA. Association of eight proteins with the enhancer creates a continuous surface for recognizing a composite DNA-binding element. Paucity of local protein-protein contacts suggests that cooperative occupancy of the enhancer comes from both binding-induced changes in DNA conformation and interactions with additional components such as CBP. Contacts with virtually every nucleotide pair account for the evolutionary invariance of the enhancer sequence.

    Organizational Affiliation: 

    The Jack and Eileen Connors Structural Biology Laboratory, Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Howard Hughes Medical Institute, 250 Longwood Avenue, Boston, MA 02115, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor p65/Interferon regulatory factor 7/Interferon regulatory factor 3 fusion proteinC [auth A]540Homo sapiensMutation(s): 1 
Gene Names: RELA
UniProt & NIH Common Fund Data Resources
Find proteins for Q14653 (Homo sapiens)
Explore Q14653 
Go to UniProtKB:  Q14653
PHAROS:  Q14653
GTEx:  ENSG00000126456 
Find proteins for Q04206 (Homo sapiens)
Explore Q04206 
Go to UniProtKB:  Q04206
PHAROS:  Q04206
GTEx:  ENSG00000173039 
Find proteins for Q92985 (Homo sapiens)
Explore Q92985 
Go to UniProtKB:  Q92985
PHAROS:  Q92985
GTEx:  ENSG00000185507 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ04206Q92985Q14653
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear factor NF-kappa-B p105 subunitD [auth B]314Homo sapiensMutation(s): 0 
Gene Names: NFKB1
UniProt & NIH Common Fund Data Resources
Find proteins for P19838 (Homo sapiens)
Explore P19838 
Go to UniProtKB:  P19838
PHAROS:  P19838
GTEx:  ENSG00000109320 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19838
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
36-MERA [auth E]36N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
34-MERB [auth F]34N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.222α = 90
b = 116.37β = 90
c = 134.237γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-12-06 
  • Released Date: 2007-07-24 
    • Deposition Author(s): Panne, D.

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-12-07
    Changes: Advisory
  • Version 1.4: 2017-08-02
    Changes: Source and taxonomy
  • Version 1.5: 2017-10-18
    Changes: Refinement description
  • Version 1.6: 2021-10-20
    Changes: Database references