2I9T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 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

  • DOI: 10.1016/s0969-2126(02)00723-2
  • Primary Citation of Related Structures:  
    2I9T

  • 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 related sites ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor p65C [auth A]279Mus musculusMutation(s): 0 
Gene Names: RelaNfkb3
UniProt
Find proteins for Q04207 (Mus musculus)
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Go to UniProtKB:  Q04207
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear factor NF-kappa-B p105 subunitD [auth B]313Mus musculusMutation(s): 0 
Gene Names: Nfkb1
UniProt & NIH Common Fund Data Resources
Find proteins for P25799 (Mus musculus)
Explore P25799 
Go to UniProtKB:  P25799
IMPC:  MGI:97312
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*CP*TP*G)-3'A [auth C]17N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*AP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*CP*AP*CP*T)-3'B [auth D]17N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.288 
      • R-Value Work: 0.233 
      • R-Value Observed: 0.233 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 97.62α = 90
      b = 166.11β = 90
      c = 60.05γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      AMoREphasing
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

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