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 1.5 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

Find similar proteins by: 
(by identity cutoff)  |  Structure
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: IRF3
Find proteins for Q14653 (Homo sapiens)
Explore Q14653 
Go to UniProtKB:  Q14653
NIH Common Fund Data Resources
PHAROS:  Q14653
GTEx:  ENSG00000126456
Find proteins for Q04206 (Homo sapiens)
Explore Q04206 
Go to UniProtKB:  Q04206
NIH Common Fund Data Resources
PHAROS:  Q04206
GTEx:  ENSG00000173039
Find proteins for Q92985 (Homo sapiens)
Explore Q92985 
Go to UniProtKB:  Q92985
NIH Common Fund Data Resources
PHAROS:  Q92985
GTEx:  ENSG00000185507
Protein Feature View
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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
Find proteins for P19838 (Homo sapiens)
Explore P19838 
Go to UniProtKB:  P19838
NIH Common Fund Data Resources
PHAROS:  P19838
GTEx:  ENSG00000109320
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
36-MERA [auth E]36N/A
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
34-MERB [auth F]34N/A
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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View more in-depth experimental data

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