1CIT

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

• PDB DOI:  https://doi.org/10.2210/pdb1CIT/pdb
• NAKB: 1CIT

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


• Deposited: 1999-04-05 Released: 1999-05-03 
• Deposition Author(s): Meinke, G., Sigler, P.B.

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Experimental Data Snapshot

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

Literature

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

Meinke, G., Sigler, P.B.

(1999) Nat Struct Biol 6: 471-477

• PubMed: 10331876 
• DOI: https://doi.org/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 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).

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.03 kDa 
• Atom Count: 1,380 
• Modelled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ORPHAN NUCLEAR RECEPTOR NGFI-B)	C [auth A]	89	Rattus norvegicus	Mutation(s): 0  Gene Names: Nr4a1, Hmr, Ngfib
UniProt
Find proteins for P22829 (Rattus norvegicus) Explore P22829  Go to UniProtKB:  P22829

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')	A [auth B]	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')	B [auth C]	16	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 53.42	α = 90
b = 34.24	β = 109.13
c = 56.26	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
MLPHARE	phasing
CNS	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-03 
Deposition Author(s): Meinke, G., Sigler, P.B.

Revision History  

• 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
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description