7OOT | pdb_00007oot

X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an interferon-stimulated response element

• PDB DOI: https://doi.org/10.2210/pdb7OOT/pdb
• NAKB: 7OOT

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-05-28 Released: 2022-06-08 
• Deposition Author(s): Agnarelli, A., El Omari, K., Alt, A.O., Mancini, E.J.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.238 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to interferon-stimulated response element

Agnarelli, A., El Omari, K., Alt, A.O., Mancini, E.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.97 kDa 
• Atom Count: 2,755 
• Modeled Residue Count: 262 
• Deposited Residue Count: 322 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon regulatory factor 4	A, B	141	Homo sapiens	Mutation(s): 0  Gene Names: IRF4, MUM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15306 (Homo sapiens) Explore Q15306  Go to UniProtKB:  Q15306
PHAROS:  Q15306 GTEx:  ENSG00000137265

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*CP*AP*AP*CP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*AP*AP*AP*GP*C)-3')	C	20	Mus musculus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3')	D [auth E]	20	Mus musculus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.238 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.78	α = 90
b = 83.25	β = 90
c = 88.53	γ = 90

Software Package:

Software Name	Purpose
xia2	data reduction
xia2	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Agnarelli, A., El Omari, K., Alt, A.O., Mancini, E.J.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	204833/Z/16/Z

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description