1NFK

STRUCTURE OF THE NUCLEAR FACTOR KAPPA-B (NF-KB) P50 HOMODIMER

• PDB DOI: https://doi.org/10.2210/pdb1NFK/pdb
• NAKB: 1NFK

• Classification: TRANSCRIPTION/DNA
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 1995-02-28 Released: 1996-12-23 
• Deposition Author(s): Ghosh, G., Van Duyne, G., Ghosh, S., Sigler, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.340 (Depositor) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Structure of NF-kappa B p50 homodimer bound to a kappa B site.

Ghosh, G., van Duyne, G., Ghosh, S., Sigler, P.B.

(1995) Nature 373: 303-310

• PubMed: 7530332 
• DOI: https://doi.org/10.1038/373303a0
• Primary Citation of Related Structures:  
  1NFK


• PubMed Abstract: 
  

  The 2.3-A crystal structure of the transcription factor NK-kappa B p50 homodimer bound to a palindromic kappa B site reveals that the Rel homology region folds into two distinct domains, similar to those in the immunoglobulin superfamily. The p50 dimer envelopes an undistorted B-DNA helix, making specific contacts along the 10-base-pair kappa B recognition site mainly through loops connecting secondary structure elements in both domains. The carboxy-terminal domains form a dimerization interface between beta-sheets using residues that are strongly conserved in the Rel family.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06510.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.89 kDa 
• Atom Count: 5,667 
• Modelled Residue Count: 646 
• Deposited Residue Count: 672 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))	C [auth A], D [auth B]	325	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P25799 (Mus musculus) Explore P25799  Go to UniProtKB:  P25799
IMPC:  MGI:97312

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*GP*GP*AP*AP*TP*TP*CP*CP*C)-3')	A [auth C], B [auth D]	11	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.340 (Depositor) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.2	α = 90
b = 132.1	β = 93.1
c = 80.1	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-12-23 
Deposition Author(s): Ghosh, G., Van Duyne, G., Ghosh, S., Sigler, P.B.

Revision History  

• Version 1.0: 1996-12-23
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary