Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 117.74 kDa 
• Atom Count: 7912 
• Residue Count: 882 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

2O61

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

• DOI: 10.2210/pdb2O61/pdb
• NDB: PD0963

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

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

Literature

An Atomic Model of the Interferon-beta Enhanceosome.

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

(2007) Cell 129: 1111-1123

• PubMed: 17574024 
• DOI: 10.1016/j.cell.2007.05.019
• Structures With Same Primary Citation


• 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. 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.

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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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Transcription factor p65/Interferon regulatory factor 7/Interferon regulatory factor 3 fusion protein	A	540	Homo sapiens	Mutation(s): 1  Gene Names: RELA
Find proteins for Q14653 (Homo sapiens) Go to UniProtKB:  Q14653
NIH Common Fund Data Resources
PHAROS  Q14653 GTEx  ENSG00000126456
Find proteins for Q04206 (Homo sapiens) Go to UniProtKB:  Q04206
NIH Common Fund Data Resources
PHAROS  Q04206 GTEx  ENSG00000173039
Find proteins for Q92985 (Homo sapiens) Go to UniProtKB:  Q92985
NIH Common Fund Data Resources
PHAROS  Q92985 GTEx  ENSG00000185507

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Nuclear factor NF-kappa-B p105 subunit	B	314	Homo sapiens	Mutation(s): 0  Gene Names: NFKB1
Find proteins for P19838 (Homo sapiens) Go to UniProtKB:  P19838
NIH Common Fund Data Resources
PHAROS  P19838 GTEx  ENSG00000109320

Entity ID: 1
Molecule	Chains	Length	Organism
36-MER	E	36	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
34-MER	F	34	N/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 = 95.222	α = 90
b = 116.37	β = 90
c = 134.237	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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
  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