1K3Z

X-ray crystal structure of the IkBb/NF-kB p65 homodimer complex

• PDB DOI:  https://doi.org/10.2210/pdb1K3Z/pdb

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


• Deposited: 2001-10-04 Released: 2002-10-04 
• Deposition Author(s): Shiva, M., Huang, D.B., Chen, Y., Huxford, T., Ghosh, S., Ghosh, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.256 
• R-Value Work: 0.181 

Literature

X-ray crystal structure of an IkappaBbeta x NF-kappaB p65 homodimer complex.

Malek, S., Huang, D.B., Huxford, T., Ghosh, S., Ghosh, G.

(2003) J Biol Chem 278: 23094-23100

• PubMed: 12686541 
• DOI: https://doi.org/10.1074/jbc.M301022200
• Primary Citation of Related Structures:  
  1K3Z, 1OY3


• PubMed Abstract: 
  

We report the crystal structure of a murine IkappaBbeta x NF-kappaB p65 homodimer complex. Crystallographic models were determined for two triclinic crystalline systems and refined against data at 2.5 and 2.1 A. The overall complex structure is similar to that of the IkappaBalpha.NF-kappaB p50/p65 heterodimer complex. One NF-kappaB p65 subunit nuclear localization signal clearly contacts IkappaBbeta, whereas a homologous segment from the second subunit of the homodimer is mostly solvent-exposed. The unique 47-amino acid insertion between ankyrin repeats three and four of IkappaBbeta is mostly disordered in the structure. Primary sequence analysis and differences in the mode of binding at the IkappaBbeta sixth ankyrin repeat and NF-kappaB p65 homodimer suggest a model for nuclear IkappaBbeta.NF-kappaB.DNA ternary complex formation. These unique structural features of IkappaBbeta may contribute to its ability to mediate persistent NF-kappaB activation.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.03 kDa 
• Atom Count: 3,769 
• Modelled Residue Count: 469 
• Deposited Residue Count: 554 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor p65	A, B	136	Mus musculus	Mutation(s): 0  Gene Names: Rela, Nfkb3
UniProt
Find proteins for Q04207 (Mus musculus) Explore Q04207  Go to UniProtKB:  Q04207

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
transcription factor inhibitor I-kappa-B-beta	C [auth D]	282	Mus musculus	Mutation(s): 5  Gene Names: Nfkbib, Ikbb
UniProt
Find proteins for Q60778 (Mus musculus) Explore Q60778  Go to UniProtKB:  Q60778

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.256 
• R-Value Work: 0.181 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.4	α = 95.17
b = 48.92	β = 91.8
c = 59.47	γ = 105.45

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-04 
Deposition Author(s): Shiva, M., Huang, D.B., Chen, Y., Huxford, T., Ghosh, S., Ghosh, G.

Revision History  

• Version 1.0: 2002-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references
• Version 1.4: 2023-08-16
  Changes: Data collection, Refinement description