1LE5

Crystal structure of a NF-kB heterodimer bound to an IFNb-kB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The X-ray crystal structure of the NF-kB p50/p65 heterodimer bound to the Interferon beta-kB site

Berkowitz, B.Huang, D.B.Chen-Park, F.E.Sigler, P.B.Ghosh, G.

(2002) J.Biol.Chem. 277: 24694-24700

  • DOI: 10.1074/jbc.M200006200
  • Primary Citation of Related Structures:  1LE9

  • PubMed Abstract: 
  • We have determined the x-ray crystal structure of the transcription factor NF-kappaB p50.p65 heterodimer complexed to kappaB DNA from the cytokine interferon beta enhancer (IFNbeta-kappaB). To better understand how the binding modes of NF-kappaB on i ...

    We have determined the x-ray crystal structure of the transcription factor NF-kappaB p50.p65 heterodimer complexed to kappaB DNA from the cytokine interferon beta enhancer (IFNbeta-kappaB). To better understand how the binding modes of NF-kappaB on its two best studied DNA targets might contribute to promoter-specific transcription, this structure is compared with the previously determined complex crystal structure containing NF-kappaB bound to the Ig kappa light chain gene enhancer as well as to a second NF-kappaB.Ig kappa light chain gene enhancer complex also reported in this paper. The global binding modes of all NF-kappaB.DNA complex structures are similar, although crystal-packing interactions lead to differences between identical complexes of the same crystallographic asymmetric unit. An extensive network of stacked amino acid side chains that contribute to base-specific DNA contacts is conserved among the three complexes. Consistent with earlier reports, however, the IFNbeta-kappaB DNA is bent significantly less by NF-kappaB than is the Ig kappa light chain gene enhancer. This and other small structural changes may play a role in explaining why NF-kappaB-directed transcription is sensitive to the context of specific promoters. The precise molecular mechanism behind the involvement of the high mobility group protein I(Y) in interferon beta enhanceosome formation remains elusive.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nuclear factor NF-kappa-B p65 subunit
A, E
274Mus musculusGene Names: Rela (Nfkb3)
Find proteins for Q04207 (Mus musculus)
Go to UniProtKB:  Q04207
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Nuclear factor NF-kappa-B p50 subunit
B, F
313Mus musculusGene Names: Nfkb1
Find proteins for P25799 (Mus musculus)
Go to UniProtKB:  P25799
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*T)-3'C,G12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3'D,H12N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.260 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 137.525α = 90.00
b = 138.015β = 97.25
c = 89.320γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance