Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | 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: 12.22 kDa 
• Atom Count: 943 
• Modelled Residue Count: 99 
• Deposited Residue Count: 106 
• Unique protein chains: 1

1U3J

Crystal structure of MLAV mutant of dimerisation domain of NF-kB p50 transcription factor

• PDB DOI: 10.2210/pdb1U3J/pdb

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


• Deposited: 2004-07-22 Released: 2004-08-17 
• Deposition Author(s): Chirgadze, D.Y., Demydchuk, M., Becker, M., Moran, S., Paoli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.222 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Snapshot of Protein Structure Evolution Reveals Conservation of Functional Dimerization through Intertwined Folding

Chirgadze, D.Y., Demydchuk, M., Becker, M., Moran, S., Paoli, M.

(2004) Structure 12: 1489-1494

• PubMed: 15296742 
• DOI: 10.1016/j.str.2004.06.011
• Primary Citation of Related Structures:  
  1U36, 1U3J, 1U3Y, 1U3Z, 1U41, 1U42


• PubMed Abstract: 
  

Protein-protein interactions govern a wide range of cellular processes. Molecular recognition responsible for homodimerization and heterodimerization in the rel/NF-kappaB family of eukaryotic transcription factors relies on a small cluster of hydrophobic residues. We have carried out a structural analysis of six NF-kappaB p50 dimer interface mutants; one of them revealed a remarkable alteration. One or possibly both its mutations cause a switch into an intertwined dimer, in which the molecular partners exchange nearly half of their fold. In spite of the extensive swapping of secondary structure elements, the topology within each counterpart is preserved, with a very similar overall structure and minimal changes at the interface. Thus intertwining rescues structure and function from a destabilizing mutation. Since the mutants originate from a directed evolution experiment and are functional, the data provide an evolutionary snapshot of how a protein structure can respond to mutations while maintaining a functional molecular architecture.

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Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear factor NF-kappa-B p105 subunit	A	106	Mus musculus	Mutation(s): 1  Gene Names: Nfkb1, 18033
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: 1.90 Å
• R-Value Free: 0.222 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.817	α = 90
b = 62.817	β = 90
c = 65.799	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-22 
• Released Date: 2004-08-17 
Deposition Author(s): Chirgadze, D.Y., Demydchuk, M., Becker, M., Moran, S., Paoli, M.

Revision History  

• Version 1.0: 2004-08-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-01
  Changes: Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references