7JFL | pdb_00007jfl

Crystal structure of human phosphorylated IRF-3 bound to CBP

• PDB DOI: https://doi.org/10.2210/pdb7JFL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-17 Released: 2020-09-09 
• Deposition Author(s): Li, P., Jing, T., Zhao, B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

The Structural Basis of IRF-3 Activation upon Phosphorylation.

Jing, T., Zhao, B., Xu, P., Gao, X., Chi, L., Han, H., Sankaran, B., Li, P.

(2020) J Immunol 205: 1886-1896

• PubMed: 32826280 
• DOI: https://doi.org/10.4049/jimmunol.2000026
• Primary Citation Related Structures: 
  7JFL, 7JFM


• PubMed Abstract: 
  

  The innate immune system is the first line of defense against bacterial and viral infections. The recognition of pathogen-associated molecular patterns by the RIG-I-like receptors, TLRs, and cGAS leads to the induction of IFN-I by activating the transcription factor IRF-3. Although the mechanism of IRF-3 activation has been extensively studied, the structural basis of IRF-3 activation upon phosphorylation is not fully understood. In this study, we determined the crystal structures of phosphorylated human and mouse IRF-3 bound to CREB-binding protein (CBP), which reveal that phosphorylated IRF-3 forms a dimer via pSer ³⁸⁶ (pSer ³⁷⁹ in mouse IRF-3) and a downstream p L x IS motif. Size-exclusion chromatography and cell-based studies show that mutations of key residues interacting with pSer ³⁸⁶ severely impair IRF-3 activation and IFN-β induction. By contrast, phosphorylation of Ser ³⁹⁶ within the p L x IS motif of human IRF-3 only plays a moderate role in IRF-3 activation. The mouse IRF-3/CBP complex structure reveals that the mechanism of mouse IRF-3 activation is similar but distinct from human IRF-3. These structural and functional studies reveal the detailed mechanism of IRF-3 activation upon phosphorylation.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843.
School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan 450002, China; and.
Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843; [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.09 kDa 
• Atom Count: 3,922 
• Modeled Residue Count: 464 
• Deposited Residue Count: 520 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon regulatory factor 3	A, C [auth B]	213	Homo sapiens	Mutation(s): 0  Gene Names: IRF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q14653 (Homo sapiens) Explore Q14653  Go to UniProtKB:  Q14653
PHAROS:  Q14653 GTEx:  ENSG00000126456

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	B [auth C], D	47	Homo sapiens	Mutation(s): 0  Gene Names: CREBBP, CBP EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens) Explore Q92793  Go to UniProtKB:  Q92793
PHAROS:  Q92793 GTEx:  ENSG00000005339

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, C [auth B]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.01	α = 90
b = 68.03	β = 106.24
c = 55.92	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Li, P., Jing, T., Zhao, B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI145287

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2020-10-07
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary