Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 73.27 kDa 
• Atom Count: 4790 
• Residue Count: 485 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2PI0

Crystal Structure of IRF-3 bound to the PRDIII-I regulatory element of the human interferon-B enhancer

• DOI: 10.2210/pdb2PI0/pdb
• NDB: PD1009

• Classification: transcription activator/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-12 Released: 2007-10-30 
• Deposition Author(s): Escalante, C.R., Nistal-Villan, E., Leyi, S., Garcia-Sastre, A., Aggarwal, A.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.264 
• R-Value Work: 0.181 
• R-Value Observed: 0.185 

Literature

Structure of IRF-3 bound to the PRDIII-I regulatory element of the human interferon-beta enhancer.

Escalante, C.R., Nistal-Villan, E., Shen, L., Garcia-Sastre, A., Aggarwal, A.K.

(2007) Mol Cell 26: 703-716

• PubMed: 17560375 
• DOI: 10.1016/j.molcel.2007.04.022
• Primary Citation of Related Structures:  
  2PI0


• PubMed Abstract: 
  

Interferon regulatory factor 3 (IRF-3) is a key transcription factor in the assembly of the mammalian interferon-beta (IFN-beta) enhanceosome. We present here the structure of IRF-3 DNA binding domain in complex with the complete PRDIII-I regulatory element of the human IFN-beta enhancer. We show that four IRF-3 molecules bind in tandem to, variably spaced, consensus and nonconsensus IRF sites on the composite element. The ability of IRF-3 to bind these variable sites derives in part from two nonconserved arginines (Arg78 and Arg86) that partake in alternate protein-DNA contacts. We also show that the protein-DNA contacts are highly overlapped and that all four IRF sites are required for gene activation in vivo. In addition, we show that changing the nonconsensus IRF sites to consensus sites creates a more efficient enhancer in vivo. Together, the structure and accompanying biological data provide insights into the assembly of the IFN-beta enhanceosome in mammals.

---

Organizational Affiliation: 

Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon regulatory factor 3	A, B, C, D	116	Homo sapiens	Mutation(s): 0  Gene Names: IRF3
Find proteins for Q14653 (Homo sapiens) Explore Q14653  Go to UniProtKB:  Q14653
NIH Common Fund Data Resources
PHAROS  Q14653 GTEx  ENSG00000126456

Entity ID: 1
Molecule	Chains	Length	Organism	Image
PRDIII-I region of human interferon-B promoter strand 1	E	32	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
PRDIII-I region of human interferon-B promoter strand 2	F	32	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.264 
• R-Value Work: 0.181 
• R-Value Observed: 0.185 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.417	α = 90
b = 46.132	β = 129.42
c = 129.325	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-12 
• Released Date: 2007-10-30 
Deposition Author(s): Escalante, C.R., Nistal-Villan, E., Leyi, S., Garcia-Sastre, A., Aggarwal, A.K.

Revision History 

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance