1J2F

X-ray crystal structure of IRF-3 and its functional implications

• PDB DOI: https://doi.org/10.2210/pdb1J2F/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-04 Released: 2003-11-25 
• Deposition Author(s): Takahasi, K., Noda, N., Horiuchi, M., Mori, M., Okabe, Y., Fukuhara, Y., Terasawa, H., Fujita, T., Inagaki, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

X-ray crystal structure of IRF-3 and its functional implications.

Takahasi, K., Suzuki, N.N., Horiuchi, M., Mori, M., Suhara, W., Okabe, Y., Fukuhara, Y., Terasawa, H., Akira, S., Fujita, T., Inagaki, F.

(2003) Nat Struct Biol 10: 922-927

• PubMed: 14555995 
• DOI: https://doi.org/10.1038/nsb1001
• Primary Citation of Related Structures:  
  1J2F


• PubMed Abstract: 
  

  Transcription factor IRF-3 is post-translationally activated by Toll-like receptor (TLR) signaling and has critical roles in the regulation of innate immunity. Here we present the X-ray crystal structure of the C-terminal regulatory domain of IRF-3(175-427) (IRF-3 175C) at a resolution of 2.3 A. IRF-3 175C is structurally similar to the Mad homology domain 2 of the Smad family. Structural and functional analyses reveal phosphorylation-induced IRF-3 dimerization, which generates an extensive acidic pocket responsible for binding with p300/CBP. Although TLR and Smad signaling are evolutionarily independent, our results suggest that IRF-3 originates from Smad and acquires its function downstream of TLR.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita 12 Nishi 6, Kita-ku, Sapporo 060-0812, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.76 kDa 
• Atom Count: 3,728 
• Modelled Residue Count: 457 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon regulatory factor 3	A, B	258	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q14653 (Homo sapiens) Explore Q14653  Go to UniProtKB:  Q14653
PHAROS:  Q14653 GTEx:  ENSG00000126456

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.808	α = 90
b = 134.808	β = 90
c = 69.34	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-25 
Deposition Author(s): Takahasi, K., Noda, N., Horiuchi, M., Mori, M., Okabe, Y., Fukuhara, Y., Terasawa, H., Fujita, T., Inagaki, F.

Revision History  

• Version 1.0: 2003-11-25
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references
• Version 1.4: 2024-10-30
  Changes: Structure summary