1RAM

A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A novel DNA recognition mode by the NF-kappa B p65 homodimer.

Chen, Y.Q.Ghosh, S.Ghosh, G.

(1998) Nat Struct Biol 5: 67-73

  • DOI: 10.1038/nsb0198-67
  • Primary Citation of Related Structures:  
    2RAM, 1RAM

  • PubMed Abstract: 
  • The crystal structure of the NF-kappa B p65 (RelA) homodimer in complex with a DNA target has been determined to 2.4 A resolution. The two p65 subunits are not symmetrically disposed on the DNA target. The homodimer should optimally bind to a pseudo-palindromic nine base pair target with each subunit recognizing a 5'GGAA-3' half site separated by a central A-T base pair ...

    The crystal structure of the NF-kappa B p65 (RelA) homodimer in complex with a DNA target has been determined to 2.4 A resolution. The two p65 subunits are not symmetrically disposed on the DNA target. The homodimer should optimally bind to a pseudo-palindromic nine base pair target with each subunit recognizing a 5'GGAA-3' half site separated by a central A-T base pair. However, one of the subunits (subunit B) encounters a half site of 5'-GAAA-3'. The single base-pair change from G-C to A-T results in highly unfavorable interactions between this half site and the base contacting protein residues in subunit B, which leads to an 18 degrees rotation of the N-terminal terminal domain from its normal conformation. Remarkably, subunit B retains all the interactions with the sugar phosphate backbone of the DNA target. This mode of interaction allows the NF-kappa B p65 homodimer to recognize DNA targets containing only one cognate half site. Differences in the sequence of the other half site provide variations in conformation and affinity of the complex.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0359, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (TRANSCRIPTION FACTOR NF-KB P65)C [auth A], D [auth B]273Mus musculusMutation(s): 0 
Gene Names: RelaNfkb3
UniProt
Find proteins for Q04207 (Mus musculus)
Explore Q04207 
Go to UniProtKB:  Q04207
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*CP*G)-3')A [auth C], B [auth D]20N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    DTT
    Query on DTT

    Download Ideal Coordinates CCD File 
    E [auth A], F [auth B]2,3-DIHYDROXY-1,4-DITHIOBUTANE
    C4 H10 O2 S2
    VHJLVAABSRFDPM-IMJSIDKUSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.324 
    • R-Value Work: 0.222 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 65.69α = 90
    b = 81.08β = 90
    c = 167.56γ = 90
    Software Package:
    Software NamePurpose
    X-PLORmodel building
    X-PLORrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    X-PLORphasing

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1998-05-27
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance