1K1A | pdb_00001k1a

Crystal structure of the ankyrin repeat domain of Bcl-3: a unique member of the IkappaB protein family

• PDB DOI: https://doi.org/10.2210/pdb1K1A/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-09-24 Released: 2001-11-21 
• Deposition Author(s): Michel, F., Soler-Lopez, M., Petosa, C., Cramer, P., Siebenlist, U., Mueller, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.229 (Depositor) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the ankyrin repeat domain of Bcl-3: a unique member of the IkappaB protein family.

Michel, F., Soler-Lopez, M., Petosa, C., Cramer, P., Siebenlist, U., Muller, C.W.

(2001) EMBO J 20: 6180-6190

• PubMed: 11707390 
• DOI: https://doi.org/10.1093/emboj/20.22.6180
• Primary Citation Related Structures: 
  1K1A, 1K1B


• PubMed Abstract: 
  

  IkappaB proteins associate with the transcription factor NF-kappaB via their ankyrin repeat domain. Bcl-3 is an unusual IkappaB protein because it is primarily nucleoplasmic and can lead to enhanced NF-kappaB-dependent transcription, unlike the prototypical IkappaB protein IkappaBalpha, which inhibits NF-kappaB activity by retaining it in the cytoplasm. Here we report the 1.9 A crystal structure of the ankyrin repeat domain of human Bcl-3 and compare it with that of IkappaBalpha bound to NF-kappaB. The two structures are highly similar over the central ankyrin repeats but differ in the N-terminal repeat and at the C-terminus, where Bcl-3 contains a seventh repeat in place of the acidic PEST region of IkappaBalpha. Differences between the two structures suggest why Bcl-3 differs from IkappaBalpha in selectivity towards various NF-kappaB species, why Bcl-3 but not IkappaBalpha can associate with its NF-kappaB partner bound to DNA, and why two molecules of Bcl-3 but only one of IkappaBalpha can bind to its NF-kappaB partner. Comparison of the two structures thus provides an insight into the functional diversity of IkappaB proteins.

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Organizational Affiliation: 
• European Molecular Biology Laboratory, Grenoble Outstation BP 181, 38042 Grenoble, Cedex 9, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.83 kDa 
• Atom Count: 1,924 
• Modeled Residue Count: 228 
• Deposited Residue Count: 241 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 3-encoded protein	A	241	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20749 (Homo sapiens) Explore P20749  Go to UniProtKB:  P20749
PHAROS:  P20749 GTEx:  ENSG00000069399

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.229 (Depositor) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.703	α = 90
b = 51.218	β = 102.01
c = 64.68	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-21 
Deposition Author(s): Michel, F., Soler-Lopez, M., Petosa, C., Cramer, P., Siebenlist, U., Mueller, C.W.

Revision History  

• Version 1.0: 2001-11-21
  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: 2023-08-16
  Changes: Data collection, Database references, Refinement description