6TD4 | pdb_00006td4

IRF4 DNA-binding domain surface entropy mutant apo structure

• PDB DOI: https://doi.org/10.2210/pdb6TD4/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-11-07 Released: 2020-11-18 
• Deposition Author(s): Tucker, J.A., Martin, M.P., Wang, L.Z., Jennings, C., Heath, R.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.245 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: other

Literature

Cancer-associated mutations in the IRF4 DNA-binding domain confer no disadvantage in DNA-binding affinity and may increase transcriptional activity

Tatum, N.J., Scott, R., Doody, G.M., Hickson, I., Jennings, C., Martin, M.P., Tooze, R.M., Tucker, J.A., Wittner, A., Wang, L.Z., Wright, E.K., Wedge, S.R., Noble, M.E.M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.97 kDa 
• Atom Count: 1,022 
• Modeled Residue Count: 107 
• Deposited Residue Count: 121 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon regulatory factor 4	A	121	Homo sapiens	Mutation(s): 4  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.245 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.874	α = 90
b = 67.457	β = 90
c = 69.884	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
REFMAC	refinement
PHENIX	refinement
xia2	data reduction
AutoSol	phasing
Coot	model building
XSCALE	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Tucker, J.A., Martin, M.P., Wang, L.Z., Jennings, C., Heath, R.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C2115/A21421

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2021-02-17
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2021-06-23
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references
• Version 1.4: 2026-03-04
  Changes: Refinement description, Structure summary