Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 75.99 kDa 
• Atom Count: 5,134 
• Modelled Residue Count: 614 
• Deposited Residue Count: 636 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

 2V2T

X-ray structure of a NF-kB p50-RelB-DNA complex

• PDB DOI: 10.2210/pdb2V2T/pdb
• NDB: NA0306

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-06-07 Released: 2007-07-03 
• Deposition Author(s): Moorthy, A.K., Huang, D.B., Wang, V.Y., Vu, D., Ghosh, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.276 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 

Literature

X-Ray Structure of a NF-kappaB p50/Relb/DNA Complex Reveals Assembly of Multiple Dimers on Tandem kappaB Sites.

Moorthy, A.K., Huang, D.B., Wang, V.Y., Vu, D., Ghosh, G.

(2007) J Mol Biol 373: 723

• PubMed: 17869269 
• DOI: 10.1016/j.jmb.2007.08.039
• Primary Citation of Related Structures:  
  2V2T


• PubMed Abstract: 
  

We describe here the X-ray crystal structure of NF-kappaB p50/RelB heterodimer bound to a kappaB DNA. Although the global modes of subunit association and kappaB DNA recognition are similar to other NF-kappaB/DNA complexes, this complex reveals distinctive features not observed for non-RelB complexes. For example, Lys274 of RelB is removed from the protein-DNA interface whereas the corresponding residues in all other subunits make base-specific contacts. This mode of binding suggests that RelB may allow the recognition of more diverse kappaB sequences. Complementary surfaces on RelB and p50, as revealed by the crystal contacts, are highly suggestive of assembly of multiple p50/RelB heterodimers on tandem kappaB sites in solution. Consistent with this model our in vitro binding experiments reveal optimal assembly of two wild-type p50/RelB heterodimers on tandem HIV kappaB DNA with 2 bp spacing but not by a mutant heterodimer where one of the RelB packing surface is altered. We suggest that multiple NF-kappaB dimers assemble at diverse kappaB promoters through direct interactions utilizing unique protein-protein interaction surfaces.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION FACTOR RELB	A	288	Mus musculus	Mutation(s): 0  Gene Names: Relb
UniProt
Find proteins for Q04863 (Mus musculus) Explore Q04863  Go to UniProtKB:  Q04863

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT	B	326	Mus musculus	Mutation(s): 0  Gene Names: Nfkb1
UniProt & NIH Common Fund Data Resources
Find proteins for P25799 (Mus musculus) Explore P25799  Go to UniProtKB:  P25799
IMPC:  MGI:97312

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.276 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.44	α = 90
b = 91.44	β = 90
c = 419.97	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-03 
Deposition Author(s): Moorthy, A.K., Huang, D.B., Wang, V.Y., Vu, D., Ghosh, G.

Revision History  

• Version 1.0: 2007-07-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance