2O61

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 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:  

  • 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 ...

    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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Transcription factor p65/Interferon regulatory factor 7/Interferon regulatory factor 3 fusion protein
A
540Homo sapiensMutation(s): 1 
Gene Names: IRF3, RELA (NFKB3), IRF7
Find proteins for Q14653 (Homo sapiens)
Go to Gene View: IRF3
Go to UniProtKB:  Q14653
Find proteins for Q04206 (Homo sapiens)
Go to Gene View: RELA
Go to UniProtKB:  Q04206
Find proteins for Q92985 (Homo sapiens)
Go to Gene View: IRF7
Go to UniProtKB:  Q92985
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Nuclear factor NF-kappa-B p105 subunit
B
314Homo sapiensMutation(s): 0 
Gene Names: NFKB1
Find proteins for P19838 (Homo sapiens)
Go to Gene View: NFKB1
Go to UniProtKB:  P19838
Entity ID: 1
MoleculeChainsLengthOrganism
36-MERE36N/A
Entity ID: 2
MoleculeChainsLengthOrganism
34-MERF34N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 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 = 90.00
b = 116.370β = 90.00
c = 134.237γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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