1VKX

CRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO THE IMMUNOGLOBULIN KB DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA.

Chen, F.E., Huang, D.B., Chen, Y.Q., Ghosh, G.

(1998) Nature 391: 410-413

  • DOI: 10.1038/34956
  • Primary Citation of Related Structures:  
    1VKX

  • PubMed Abstract: 

    • The NF-kappaB p50/p65 heterodimer is the classical member of the Rel family of transcription factors which regulate diverse cellular functions such as immune response, cell growth, and development. Other mammalian Rel family members, including the proteins p52, proto-oncoprotein c-Rel, and RelB, all have amino-terminal Rel-homology regions (RHRs) ...

    The NF-kappaB p50/p65 heterodimer is the classical member of the Rel family of transcription factors which regulate diverse cellular functions such as immune response, cell growth, and development. Other mammalian Rel family members, including the proteins p52, proto-oncoprotein c-Rel, and RelB, all have amino-terminal Rel-homology regions (RHRs). The RHR is responsible for the dimerization, DNA binding and cytosolic localization of these proteins by virtue of complex formation with inhibitor kappaB proteins. Signal-induced removal of kappaB inhibitors allows translocation of dimers to the cell nucleus and transcriptional regulation of kappaB DNA-containing genes. NF-kappaB specifically recognizes kappaB DNA elements with a consensus sequence of 5'-GGGRNYYYCC-3' (R is an unspecified purine; Y is an unspecified pyrimidine; and N is any nucleotide). Here we report the crystal structure at 2.9 A resolution of the p50/p65 heterodimer bound to the kappaB DNA of the intronic enhancer of the immunoglobulin light-chain gene. Our structure reveals a 5-base-pair 5' subsite for p50, and a 4-base-pair 3' subsite for p65. This structure indicates why the p50/p65 heterodimer interface is stronger than that of either homodimer. A comparison of this structure with those of other Rel dimers reveals that both subunits adopt variable conformations in a DNA-sequence-dependent manner. Our results explain the different behaviour of the p50/p65 heterodimer with heterologous promoters.

    Related Citations: 
    • Structure of NF-Kb p50 Homodimer Bound to a Kb Site
      Ghosh, G., Duyne, G.V., Ghosh, S., Sigler, P.B.
      (1995) Nature 373: 303
    Organizational Affiliation: 

    Department of Biology, University of California, San Diego, La Jolla 92093-0359, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (NF-KAPPA B P65 SUBUNIT)C [auth A]273Mus musculusMutation(s): 0 
Gene Names: Rela, Nfkb3
UniProt
Find proteins for Q04207 (Mus musculus)
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Go to UniProtKB:  Q04207
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UniProt GroupQ04207
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (NF-KAPPA B P50 SUBUNIT)D [auth B]312Mus 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
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UniProt GroupP25799
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*C)-3')A [auth C]12N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*C)-3')B [auth D]12N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.61α = 90
b = 106.61β = 90
c = 206.56γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-12-09
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance