9BDX

NF-kappaB RelA homo-dimer bound to CG-centric kappaB DNA

• PDB DOI: https://doi.org/10.2210/pdb9BDX/pdb
• NAKB: 9BDX

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


• Deposited: 2024-04-12 Released: 2024-04-24 
• Deposition Author(s): Biswas, T., Shahabi, S., Tsodikov, O.V., Ghosh, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.374 
• R-Value Work: 0.321 
• R-Value Observed: 0.324 

Literature

Transient interactions modulate affinity of NF-kappaB transcription factors for DNA

Biswas, T., Shandy, S., Tsodikov, O.V., Huang, D., Li, T., Wang, Y., Wang, V., Ghosh, G.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 77.39 kDa 
• Atom Count: 5,080 
• Modelled Residue Count: 584 
• Deposited Residue Count: 612 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor p65	A, B	287	Mus musculus	Mutation(s): 0  Gene Names: Rela, Nfkb3
UniProt
Find proteins for Q04207 (Mus musculus) Explore Q04207  Go to UniProtKB:  Q04207

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*TP*GP*GP*GP*AP*AP*CP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3')	C	19	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*GP*TP*TP*CP*CP*CP*AP*GP*T)-3')	D	19	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.374 
• R-Value Work: 0.321 
• R-Value Observed: 0.324 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.953	α = 90
b = 132.182	β = 90
c = 66.577	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Biswas, T., Shahabi, S., Tsodikov, O.V., Ghosh, G.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM085490-11

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release