1SVC

NFKB P50 HOMODIMER BOUND TO DNA

• PDB DOI: https://doi.org/10.2210/pdb1SVC/pdb
• NAKB: 1SVC

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 1995-11-27 Released: 1996-06-10 
• Deposition Author(s): Mueller, C.W., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.286 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 

Literature

Structure of the NF-kappa B p50 homodimer bound to DNA.

Muller, C.W., Rey, F.A., Sodeoka, M., Verdine, G.L., Harrison, S.C.

(1995) Nature 373: 311-317

• PubMed: 7830764 
• DOI: https://doi.org/10.1038/373311a0
• Primary Citation of Related Structures:  
  1SVC


• PubMed Abstract: 
  

  The structure of a large fragment of the p50 subunit of the human transcription factor NF-kappa B, bound as a homodimer to DNA, reveals that the Rel-homology region has two beta-barrel domains that grip DNA in the major groove. Both domains contact the DNA backbone. The amino-terminal specificity domain contains a recognition loop that interacts with DNA bases; the carboxy-terminal dimerization domain bears the site of I-kappa B interaction. The folds of these domains are related to immunoglobulin-like modules. The amino-terminal domain also resembles the core domain of p53.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Cambridge, Massachusetts 02138.

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: 47.01 kDa 
• Atom Count: 2,903 
• Modelled Residue Count: 330 
• Deposited Residue Count: 384 
• 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))	B [auth P]	365	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P19838 (Homo sapiens) Explore P19838  Go to UniProtKB:  P19838
PHAROS:  P19838 GTEx:  ENSG00000109320

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*AP*TP*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*CP*TP*A P*GP*A)-3')	A [auth D]	19	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.286 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137	α = 90
b = 137	β = 90
c = 57	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-06-10 
Deposition Author(s): Mueller, C.W., Harrison, S.C.

Revision History  

• Version 1.0: 1996-06-10
  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: 2021-11-03
  Changes: Database references
• Version 1.4: 2024-02-14
  Changes: Data collection