3DO7

X-ray structure of a NF-kB p52/RelB/DNA complex

• PDB DOI: https://doi.org/10.2210/pdb3DO7/pdb
• NAKB: 3DO7

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


• Deposited: 2008-07-03 Released: 2009-07-21 
• Deposition Author(s): Fusco, A., Huang, D.B., Miller, D., Vu, D., Ghosh, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.273 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Literature

NF-kapppaB p52:RelB heterodimer uses different binding modes to recognize different kappaB DNA

Fusco, A., Huang, D.B., Miller, D., Vu, D., Ghosh, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.54 kDa 
• Atom Count: 5,288 
• Modelled Residue Count: 621 
• Deposited Residue Count: 622 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Avian reticuloendotheliosis viral (V-rel) oncogene related B	D [auth A]	296	Mus musculus	Mutation(s): 0  Gene Names: Relb
UniProt
Find proteins for Q04863 (Mus musculus) Explore Q04863  Go to UniProtKB:  Q04863

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear factor NF-kappa-B p100 subunit	E [auth B]	293	Homo sapiens	Mutation(s): 0  Gene Names: NFKB2, LYT10
UniProt & NIH Common Fund Data Resources
Find proteins for Q00653 (Homo sapiens) Explore Q00653  Go to UniProtKB:  Q00653
PHAROS:  Q00653 GTEx:  ENSG00000077150

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'	A [auth C], B [auth D], C [auth E]	11	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.273 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.64	α = 90
b = 124.13	β = 90
c = 189.59	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Fusco, A., Huang, D.B., Miller, D., Vu, D., Ghosh, G.

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary