Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26403.76 
• Atom Count: 1660 
• Residue Count: 228 
• Unique protein chains: 1

1MY5

NF-kappaB p65 subunit dimerization domain homodimer

• DOI: 10.2210/pdb1MY5/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2002-10-03 Released: 2002-12-04 
• Deposition Author(s): Huxford, T., Mishler, D., Phelps, C.B., Huang, D.-B., Sengchanthalangsy, L.L., Reeves, R., Hughes, C.A., Komives, E.A., Ghosh, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.221 
• R-Value Work: 0.200 

Literature

Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/I kappaB alpha complex formation

Huxford, T., Mishler, D., Phelps, C.B., Huang, D.-B., Sengchanthalangsy, L.L., Reeves, R., Hughes, C.A., Komives, E.A., Ghosh, G.

(2002) J.Mol.Biol. 324: 587-597

• PubMed: 12460563 
• Primary Citation of Related Structures:  
  1MY7


• PubMed Abstract: 
  

IkappaBalpha inhibits transcription factor NF-kappaB activity by specific binding to NF-kappaB heterodimers composed of p65 and p50 subunits. It binds with slightly lower affinity to p65 homodimers and with significantly lower affinity to homodimers of p50. We have employed a structure-based mutagenesis approach coupled with protein-protein interaction assays to determine the source of this dimer selectivity exhibited by IkappaBalpha. Mutation of amino acid residues in IkappaBalpha that contact NF-kappaB only marginally affects complex binding affinity, indicating a lack of hot spots in NF-kappaB/IkappaBalpha complex formation. Conversion of the weak binding NF-kappaB p50 homodimer into a high affinity binding partner of IkappaBalpha requires transfer of both the NLS polypeptide and amino acid residues Asn202 and Ser203 from the NF-kappaB p65 subunit. Involvement of Asn202 and Ser203 in complex formation is surprising as these amino acid residues occupy solvent exposed positions at a distance of 20A from IkappaBalpha in the crystal structures. However, the same amino acid residue positions have been genetically isolated as determinants of binding specificity in a homologous system in Drosophila. X-ray crystallographic and solvent accessibility experiments suggest that these solvent-exposed amino acid residues contribute to NF-kappaB/IkappaBalpha complex formation by modulating the NF-kappaB p65 subunit NLS polypeptide.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NF-kappaB p65 (RelA) subunit	A, B	114	Mus musculus	Mutation(s): 0  Gene Names: Rela (Nfkb3)
Find proteins for Q04207 (Mus musculus) Go to UniProtKB:  Q04207

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.221 
• R-Value Work: 0.200 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.348	α = 90.00
b = 74.732	β = 90.00
c = 109.147	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
CNS	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-10-03 
• Released Date: 2002-12-04 
• Deposition Author(s): Huxford, T., Mishler, D., Phelps, C.B., Huang, D.-B., Sengchanthalangsy, L.L., Reeves, R., Hughes, C.A., Komives, E.A., Ghosh, G.

Revision History 

• Version 1.0: 2002-12-04
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance