› 9bdx

X-ray diffraction
3.6Å resolution

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

Released:
DOI: 10.2210/pdb9bdx/pdb
Model geometry
Fit model/data
PDB entry 9bdx coloured by chain, front view.
PDB entry 9bdx coloured by chain, side view.
PDB entry 9bdx coloured by chain, top view.
Source organisms:
Primary publication:
Transient interactions modulate the affinity of NF-κB transcription factors for DNA.
Li T, Shahabi S, Biswas T, Tsodikov OV, Pan W, Huang DB, Wang VY, Wang Y, Ghosh G
Proc Natl Acad Sci U S A 121 e2405555121 (2024)
PMID: 38805268

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-271037 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcription factor p65 Chains: A, B
Molecule details ›
Chains: A, B
Length: 287 amino acids
Theoretical weight: 32.87 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q04207 (Residues: 19-304; Coverage: 52%)
Gene names: Nfkb3, Rela
Sequence domains:
DNA (5'-D(P*AP*CP*TP*GP*GP*GP*AP*AP*CP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 5.84 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*GP*TP*TP*CP*CP*CP*AP*GP*T)-3') Chain: D

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P21212
Unit cell:
a: 113.953Å b: 132.182Å c: 66.577Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.324 0.321 0.374
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO