Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20027.15 
• Atom Count: 1342 
• Residue Count: 121 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1CIT

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

• DOI: 10.2210/pdb1CIT/pdb
• NDB: PD0046

• Classification: TRANSCRIPTION/DNA
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)


• 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: 2.7 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.Mol.Biol. 6: 471-477

• PubMed: 10331876 
• 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 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DNA	Kd: 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 = 53.420	α = 90.00
b = 34.240	β = 109.13
c = 56.260	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-04-05 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance