2V2T

X-ray structure of a NF-kB p50-RelB-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-Ray Structure of a NF-kappaB p50/Relb/DNA Complex Reveals Assembly of Multiple Dimers on Tandem kappaB Sites.

Moorthy, A.K.Huang, D.B.Wang, V.Y.Vu, D.Ghosh, G.

(2007) J.Mol.Biol. 373: 723

  • DOI: 10.1016/j.jmb.2007.08.039

  • PubMed Abstract: 
  • We describe here the X-ray crystal structure of NF-kappaB p50/RelB heterodimer bound to a kappaB DNA. Although the global modes of subunit association and kappaB DNA recognition are similar to other NF-kappaB/DNA complexes, this complex reveals disti ...

    We describe here the X-ray crystal structure of NF-kappaB p50/RelB heterodimer bound to a kappaB DNA. Although the global modes of subunit association and kappaB DNA recognition are similar to other NF-kappaB/DNA complexes, this complex reveals distinctive features not observed for non-RelB complexes. For example, Lys274 of RelB is removed from the protein-DNA interface whereas the corresponding residues in all other subunits make base-specific contacts. This mode of binding suggests that RelB may allow the recognition of more diverse kappaB sequences. Complementary surfaces on RelB and p50, as revealed by the crystal contacts, are highly suggestive of assembly of multiple p50/RelB heterodimers on tandem kappaB sites in solution. Consistent with this model our in vitro binding experiments reveal optimal assembly of two wild-type p50/RelB heterodimers on tandem HIV kappaB DNA with 2 bp spacing but not by a mutant heterodimer where one of the RelB packing surface is altered. We suggest that multiple NF-kappaB dimers assemble at diverse kappaB promoters through direct interactions utilizing unique protein-protein interaction surfaces.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSCRIPTION FACTOR RELB
A
288Mus musculusGene Names: Relb
Find proteins for Q04863 (Mus musculus)
Go to UniProtKB:  Q04863
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT
B
326Mus musculusGene Names: Nfkb1
Find proteins for P25799 (Mus musculus)
Go to UniProtKB:  P25799
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*CP*CP*CP)-3'C,D11N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.238 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.440α = 90.00
b = 91.440β = 90.00
c = 419.970γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
AMoREphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance