1CIT

DNA-BINDING MECHANISM OF THE MONOMERIC ORPHAN NUCLEAR RECEPTOR NGFI-B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B.

Meinke, G.Sigler, P.B.

(1999) Nat Struct Biol 6: 471-477

  • DOI: 10.1038/8276
  • Primary Citation of Related Structures:  
    1CIT

  • PubMed Abstract: 
  • The 2.7 A X-ray crystal structure of the DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B), complexed to its high-affinity DNA target, represents the first structure analysis of a nuclear receptor DBD bound as a monomer to DNA ...

    The 2.7 A X-ray crystal structure of the DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B), complexed to its high-affinity DNA target, represents the first structure analysis of a nuclear receptor DBD bound as a monomer to DNA. The structure of the core DBD and its interactions with the major groove of the DNA are similar to previously crystallographically solved DBD-DNA complexes in this superfamily; however, residues C-terminal to this core form a separate and unique substructure that interacts extensively and in a sequence-specific way with the minor groove of its DNA target, in particular with the characteristic 3 A-T base-pair identity element that extends 5' to the usual nuclear receptor half-site (AGGTCA).


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry and the Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06511, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ORPHAN NUCLEAR RECEPTOR NGFI-B)C [auth A]89Rattus norvegicusMutation(s): 0 
Gene Names: Nr4a1HmrNgfib
UniProt
Find proteins for P22829 (Rattus norvegicus)
Explore P22829 
Go to UniProtKB:  P22829
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')A [auth B]16N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')B [auth C]16N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      D [auth A], E [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Binding Affinity Annotations 
      IDSourceBinding Affinity
      DNA PDBBind:  1CIT Kd: 1 (nM) from 1 assay(s)
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.70 Å
      • R-Value Free: 0.295 
      • R-Value Work: 0.219 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 53.42α = 90
      b = 34.24β = 109.13
      c = 56.26γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      X-PLORmodel building
      MLPHAREphasing
      CNSrefinement
      X-PLORphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1999-05-03
        Type: Initial release
      • Version 1.1: 2007-10-16
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance