7JM4 image
Deposition Date 2020-07-31
Release Date 2021-03-24
Last Version Date 2023-10-18
Entry Detail
PDB ID:
7JM4
Keywords:
Title:
IRF Transcription Factor
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.95 Å
R-Value Free:
0.20
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Interferon regulatory factor 4
Gene (Uniprot):IRF4
Chain IDs:C (auth: B), D (auth: A), G, H
Chain Length:111
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:Interferon-Stimulated Response Elements
Chain IDs:A (auth: D), E (auth: C)
Chain Length:19
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:Interferon-Stimulated Response Elements
Chain IDs:B (auth: E), F
Chain Length:19
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structural determinants of the IRF4/DNA homodimeric complex.
Nucleic Acids Res. 49 2255 2265 (2021)
PMID: 33533913 DOI: 10.1093/nar/gkaa1287

Abstact

Interferon regulatory factor 4 (IRF4) is a key transcription factor (TF) in the regulation of immune cells, including B and T cells. It acts by binding DNA as both a homodimer and, in conjunction with other TFs, as a heterodimer. The choice of homo and heterodimeric/ DNA interactions is a critical aspect in the control of the transcriptional program and cell fate outcome. To characterize the nature of this interaction in the homodimeric complex, we have determined the crystal structure of the IRF4/ISRE homodimeric complex. We show that the complex formation is aided by a substantial DNA deformation with co-operative binding achieved exclusively through protein-DNA contact. This markedly contrasts with the heterodimeric form where DNA bound IRF4 is shown to physically interact with PU.1 TF to engage EICE1. We also show that the hotspot residues (Arg98, Cys99 and Asn102) contact both consensus and non-consensus sequences with the L1 loop exhibiting marked flexibility. Additionally, we identified that IRF4L116R, a mutant associated with chronic lymphocytic leukemia, binds more robustly to DNA thereby providing a rationale for the observed gain of function. Together, we demonstrate key structural differences between IRF4 homo and heterodimeric complexes, thereby providing molecular insights into IRF4-mediated transcriptional regulation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures