Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.15 kDa 
• Atom Count: 2550 
• Modelled Residue Count: 293 
• Deposited Residue Count: 348 
• Unique protein chains: 1

3QU6

Crystal structure of IRF-3 DBD free form

• DOI: 10.2210/pdb3QU6/pdb

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


• Deposited: 2011-02-23 Released: 2011-06-01 
• Deposition Author(s): De Ioannes, P.E., Escalante, C.R., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.263 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

Structures of apo IRF-3 and IRF-7 DNA binding domains: effect of loop L1 on DNA binding.

De Ioannes, P., Escalante, C.R., Aggarwal, A.K.

(2011) Nucleic Acids Res 39: 7300-7307

• PubMed: 21596780 
• DOI: 10.1093/nar/gkr325
• Primary Citation of Related Structures:  
  3QU3, 3QU6


• PubMed Abstract: 
  

Interferon regulatory factors IRF-3 and IRF-7 are transcription factors essential in the activation of interferon-β (IFN-β) gene in response to viral infections. Although, both proteins recognize the same consensus IRF binding site AANNGAAA, they have distinct DNA binding preferences for sites in vivo. The X-ray structures of IRF-3 and IRF-7 DNA binding domains (DBDs) bound to IFN-β promoter elements revealed flexibility in the loops (L1-L3) and the residues that make contacts with the target sequence. To characterize the conformational changes that occur on DNA binding and how they differ between IRF family members, we have solved the X-ray structures of IRF-3 and IRF-7 DBDs in the absence of DNA. We found that loop L1, carrying the conserved histidine that interacts with the DNA minor groove, is disordered in apo IRF-3 but is ordered in apo IRF-7. This is reflected in differences in DNA binding affinities when the conserved histidine in loop L1 is mutated to alanine in the two proteins. The stability of loop L1 in IRF-7 derives from a unique combination of hydrophobic residues that pack against the protein core. Together, our data show that differences in flexibility of loop L1 are an important determinant of differential IRF-DNA binding.

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Organizational Affiliation: 

Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, NY 10029, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IRF3 protein	A, B, C	116	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A],  E [auth A],  F [auth A],  G [auth A],  N [auth B],  O [auth B],  R [auth C],  S [auth C],  T [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	H [auth A], I [auth A], J [auth A], M [auth A], P [auth B], U [auth C], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	K [auth A], L [auth A], Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.263 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.908	α = 90
b = 64.908	β = 90
c = 157.621	γ = 120

Software Package:

Software Name	Purpose
JDirector	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-23 
• Released Date: 2011-06-01 
Deposition Author(s): De Ioannes, P.E., Escalante, C.R., Aggarwal, A.K.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-09-14
  Changes: Database references