Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.26 kDa 
• Atom Count: 936 
• Modelled Residue Count: 106 
• Deposited Residue Count: 106 
• Unique protein chains: 1

1BFS

STRUCTURE OF NF-KB P50 HOMODIMER BOUND TO A KB SITE

• PDB DOI: 10.2210/pdb1BFS/pdb

• Classification: TRANSCRIPTION FACTOR
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 1997-09-12 Released: 1998-01-28 
• Deposition Author(s): Huang, D.B., Huxford, T., Chen, Y.Q., Ghosh, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.287 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 

Literature

The role of DNA in the mechanism of NFkappaB dimer formation: crystal structures of the dimerization domains of the p50 and p65 subunits.

Huang, D.B., Huxford, T., Chen, Y.Q., Ghosh, G.

(1997) Structure 5: 1427-1436

• PubMed: 9384558 
• DOI: 10.1016/s0969-2126(97)00293-1
• Primary Citation of Related Structures:  
  1BFS, 1BFT


• PubMed Abstract: 
  

Members of the rel/NFkappaB family of transcription factors play a vital role in the regulation of rapid cellular responses, such as those required to fight infection or react to cellular stress. Members of this family of proteins form homo- and heterodimers with differing affinities for dimerization. They share a structural motif known as the rel homology region (RHR), the C-terminal one third of which mediates protein dimerization. Crystal structures of the rel/NFkappaB family members p50 and p65 in their DNA-bound homodimeric form have been solved. These structures showed that the residues from the dimerization domains of both p50 and p65 participate in DNA binding and that the DNA-protein and protein dimerization surfaces form one continuous overlapping interface. We desired to investigate the contribution of DNA to NFkappaB dimerization and to identify the mechanism for the selective association of rel/NFkappaB family peptides into transcriptionally active dimers.

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Related Citations: 

• Structure of NF-Kappa B p50 Homodimer Bound to a Kappa B Site
  Ghosh, G., Van Duyne, G., Ghosh, S., Sigler, P.B.
  (1995) Nature 373: 303

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0359, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR FACTOR NF-KAPPA-B P50	A	106	Mus musculus	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.287 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.33	α = 90
b = 62.33	β = 90
c = 65.74	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-09-12 
• Released Date: 1998-01-28 
Deposition Author(s): Huang, D.B., Huxford, T., Chen, Y.Q., Ghosh, G.

Revision History  

• Version 1.0: 1998-01-28
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance