1A3Q

HUMAN NF-KAPPA-B P52 BOUND TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1093/emboj/16.23.7078

  • 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 diffe ...

    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.


    Related Citations: 
    • Engineering of Diffraction-Quality Crystals of the NF-kappaB P52 Homodimer:DNA Complex
      Cramer, P.,Muller, C.W.
      (1997) FEBS Lett. 405: 373


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (NUCLEAR FACTOR KAPPA-B P52)
A, B
285Homo sapiensMutation(s): 0 
Gene Names: NFKB2 (LYT10)
Find proteins for Q00653 (Homo sapiens)
Go to Gene View: NFKB2
Go to UniProtKB:  Q00653
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*C)-3')C11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*GP*GP*AP*TP*TP*CP*CP*CP*C)-3')D11N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.200α = 90.00
b = 121.000β = 90.00
c = 134.900γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-11
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance