2IRF

CRYSTAL STRUCTURE OF AN IRF-2/DNA COMPLEX.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences.

Fujii, Y.Shimizu, T.Kusumoto, M.Kyogoku, Y.Taniguchi, T.Hakoshima, T.

(1999) EMBO J. 18: 5028-5041

  • DOI: 10.1093/emboj/18.18.5028

  • PubMed Abstract: 
  • There has been growing interest in the role of the IRF (interferon regulatory factor) family of transcription factors in the regulation of immune responses, cytokine signaling, and oncogenesis. These members are characterized by their well-conserved ...

    There has been growing interest in the role of the IRF (interferon regulatory factor) family of transcription factors in the regulation of immune responses, cytokine signaling, and oncogenesis. These members are characterized by their well-conserved DNA binding domains at the N-terminal regions. Here we report the 2.2 A resolution crystal structure of the DNA binding domain of one such family member, IRF-2, bound to DNA. The structure reveals its recognition sequence, AANNGAAA (here, recognized bases are underlined and in bold, and N indicates any base), and its cooperative binding to a tandem repeat of the GAAA core sequence induced by DNA structure distortions. These facts explain well the diverse binding properties of the IRF family members, which bind to both single and tandemly repeated sequences. Furthermore, we also identified the 'helix-hairpin-strand motif' at the C terminus of the recognition helix as a metal binding site that is commonly found in certain classes of DNA-interactive proteins. Our results provide new insights into the structure and function of this family of transcription factors.


    Organizational Affiliation

    Department of Molecular Biology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
INTERFERON REGULATORY FACTOR 2
G, H, I, J, K, L
113Mus musculusMutation(s): 0 
Gene Names: Irf2
Find proteins for P23906 (Mus musculus)
Go to UniProtKB:  P23906
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3')A,B,C12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3')D,E,F13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
G, H, I, J, K, L
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5IU
Query on 5IU
A, B, C, D, E, F
DNA LINKINGC9 H12 I N2 O8 PDU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 170 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 132.300α = 90.00
b = 132.300β = 90.00
c = 296.500γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-08
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance