Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 72.77 kDa 
• Atom Count: 4979 
• Modelled Residue Count: 612 
• Deposited Residue Count: 641 
• Unique protein chains: 3

1IKN

IKAPPABALPHA/NF-KAPPAB COMPLEX

• DOI: 10.2210/pdb1IKN/pdb

• Classification: TRANSCRIPTION FACTOR
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-11-13 Released: 1999-04-12 
• Deposition Author(s): Huxford, T., Huang, D.-B., Malek, S., Ghosh, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.223 

Literature

The crystal structure of the IkappaBalpha/NF-kappaB complex reveals mechanisms of NF-kappaB inactivation.

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

(1998) Cell 95: 759-770

• PubMed: 9865694 
• DOI: 10.1016/s0092-8674(00)81699-2
• Primary Citation of Related Structures:  
  1IKN


• PubMed Abstract: 
  

IkappaBalpha regulates the transcription factor NF-kappaB through the formation of stable IkappaBalpha/NF-kappaB complexes. Prior to induction, IkappaBalpha retains NF-kappaB in the cytoplasm until the NF-kappaB activation signal is received. After activation, NF-kappaB is removed from gene promoters through association with nuclear IkappaBalpha, restoring the preinduction state. The 2.3 A crystal structure of IkappaBalpha in complex with the NF-kappaB p50/p65 heterodimer reveals mechanisms of these inhibitory activities. The presence of IkappaBalpha allows large en bloc movement of the NF-kappaB p65 subunit amino-terminal domain. This conformational change induces allosteric inhibition of NF-kappaB DNA binding. Amino acid residues immediately preceding the nuclear localization signals of both NF-kappaB p50 and p65 subunits are tethered to the IkappaBalpha amino-terminal ankyrin repeats, impeding NF-kappaB from nuclear import machinery recognition.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (NF-KAPPA-B P65 SUBUNIT)	A	286	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
PROTEIN (NF-KAPPA-B P50D SUBUNIT)	B [auth C]	119	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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (I-KAPPA-B-ALPHA)	C [auth D]	236	Homo sapiens	Mutation(s): 0  Gene Names: MAD-3, NFKBIA, IKBA, MAD3, NFKBI
UniProt & NIH Common Fund Data Resources
Find proteins for P25963 (Homo sapiens) Explore P25963  Go to UniProtKB:  P25963
PHAROS:  P25963 GTEx:  ENSG00000100906

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.223 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.5	α = 90
b = 49.3	β = 108.7
c = 120.6	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-11-13 
• Released Date: 1999-04-12 
Deposition Author(s): Huxford, T., Huang, D.-B., Malek, S., Ghosh, G.

Revision History  

• Version 1.0: 1999-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance