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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 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.Mol.Biol. 6: 471-477

  • DOI: 10.1038/8276

  • 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 bou ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ORPHAN NUCLEAR RECEPTOR NGFI-B)
A
89Rattus norvegicusMutation(s): 0 
Gene Names: Nr4a1 (Hmr, Ngfib)
Find proteins for P22829 (Rattus norvegicus)
Go to UniProtKB:  P22829
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')B16N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')C16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.420α = 90.00
b = 34.240β = 109.13
c = 56.260γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
X-PLORphasing
CNSrefinement
DENZOdata reduction
X-PLORmodel building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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