2I9T

Structure of NF-kB p65-p50 heterodimer bound to PRDII element of B-interferon promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter

Escalante, C.R.Shen, L.Thanos, D.Aggarwal, A.K.

(2002) Structure 10: 383-391


  • PubMed Abstract: 
  • Upon viral infection, NF-kappaB translocates to the nucleus and activates the IFN-beta gene by binding to the PRDII element. Strikingly, NF-kappaB loses its ability to activate the IFN-beta gene when the PRDII element is substituted by closely relate ...

    Upon viral infection, NF-kappaB translocates to the nucleus and activates the IFN-beta gene by binding to the PRDII element. Strikingly, NF-kappaB loses its ability to activate the IFN-beta gene when the PRDII element is substituted by closely related sites. We report here the crystal structure of NF-kappaB p50/p65 heterodimer bound to the PRDII element from the IFN-beta promoter. The structure reveals an unexpected alteration in configuration, in which the p50 specificity domain moves by as much as approximately 9 A when compared to NF-kappaB heterodimer bound to the immunoglobulin kappaB site (Ig-kappaB) while maintaining the same base-specific contacts with the DNA. Taken together, the structure offers new insights into the allosteric effects of closely related DNA sites on the configuration of NF-kappaB and its transcriptional selectivity.


    Organizational Affiliation

    Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Transcription factor p65
A
279Mus musculusMutation(s): 0 
Gene Names: Rela (Nfkb3)
Find proteins for Q04207 (Mus musculus)
Go to UniProtKB:  Q04207
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Nuclear factor NF-kappa-B p105 subunit
B
313Mus musculusMutation(s): 0 
Gene Names: Nfkb1
Find proteins for P25799 (Mus musculus)
Go to UniProtKB:  P25799
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*CP*TP*G)-3'C17N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*AP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*CP*AP*CP*T)-3'D17N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 97.620α = 90.00
b = 166.110β = 90.00
c = 60.050γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
HKL-2000data collection
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Structure summary