1A3Q

HUMAN NF-KAPPA-B P52 BOUND TO DNA

• PDB DOI: https://doi.org/10.2210/pdb1A3Q/pdb
• NAKB: 1A3Q

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


• Deposited: 1998-01-23 Released: 1998-06-11 
• Deposition Author(s): Cramer, P., Larson, C.J., Verdine, G.L., Muller, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.320 
• R-Value Work: 0.219 

Literature

Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution.

Cramer, P., Larson, C.J., Verdine, G.L., Muller, C.W.

(1997) EMBO J 16: 7078-7090

• PubMed: 9384586 
• DOI: https://doi.org/10.1093/emboj/16.23.7078
• Primary Citation of Related Structures:  
  1A3Q


• PubMed Abstract: 
  

  The crystal structure of human NF-kappaB p52 in its specific complex with the natural kappaB DNA binding site MHC H-2 has been solved at 2.1 A resolution. Whereas the overall structure resembles that of the NF-kappaB p50-DNA complex, pronounced differences are observed within the 'insert region'. This sequence segment differs in length between different Rel proteins. Compared with NF-kappaB p50, the compact alpha-helical insert region element is rotated away from the core of the N-terminal domain, opening up a mainly polar cleft. The insert region presents potential interaction surfaces to other proteins. The high resolution of the structure reveals many water molecules which mediate interactions in the protein-DNA interface. Additional complexity in Rel protein-DNA interaction comes from an extended interfacial water cavity that connects residues at the edge of the dimer interface to the central DNA bases. The observed water network might acount for differences in binding specificity between NF-kappaB p52 and NF-kappaB p50 homodimers.

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Organizational Affiliation: 

European Molecular Biology Laboratory (EMBL), Grenoble Outstation, c/o ILL, BP 156, 38042 Grenoble Cedex 9, France.

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: 71.12 kDa 
• Atom Count: 5,748 
• Modelled Residue Count: 592 
• Deposited Residue Count: 592 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (NUCLEAR FACTOR KAPPA-B P52)	C [auth A], D [auth B]	285	Homo sapiens	Mutation(s): 0
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
DNA (5'-D(*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*C)-3')	A [auth C]	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*GP*AP*TP*TP*CP*CP*CP*C)-3')	B [auth D]	11	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.320 
• R-Value Work: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.2	α = 90
b = 121	β = 90
c = 134.9	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-11 
Deposition Author(s): Cramer, P., Larson, C.J., Verdine, G.L., Muller, C.W.

Revision History  

• Version 1.0: 1998-06-11
  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: 2024-02-07
  Changes: Data collection, Database references