1A6Y | pdb_00001a6y

REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1A6Y/pdb
• NAKB: 1A6Y

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1998-03-04 Released: 1998-10-21 
• Deposition Author(s): Zhao, Q., Khorasanizadeh, S., Rastinejad, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.288 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.215 (DCC) 

Starting Model: experimental

Literature

Structural elements of an orphan nuclear receptor-DNA complex.

Zhao, Q., Khorasanizadeh, S., Miyoshi, Y., Lazar, M.A., Rastinejad, F.

(1998) Mol Cell 1: 849-861

• PubMed: 9660968 
• DOI: https://doi.org/10.1016/s1097-2765(00)80084-2
• Primary Citation Related Structures: 
  1A6Y


• PubMed Abstract: 
  

  The nuclear hormone receptors form the largest known family of transcription factors. The current notion of receptor DNA discrimination, based solely on one major type of hexameric half-site and a highly conserved 66-residue core DNA-binding domain (DBD), does not adequately describe how more than 150 nonsteroid receptors differentiate among response elements. Here, we describe the 2.3 A crystal structure of the DNA-binding region of the orphan receptor RevErb arranged as a tandem homodimer on its optimal response element. The structure reveals the presence of a second major protein-DNA interface adjacent to the classical one involving the half-sites. A sequence comparison of orphan receptors suggests that unique minor-groove interactions involving the receptor hinge regions impart the necessary DNA and dimerization specificity.

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Organizational Affiliation: 
• Department of Pharmacology, School of Medicine, University of Virginia, Charlottesville 22908, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.45 kDa 
• Atom Count: 2,334 
• Modeled Residue Count: 202 
• Deposited Residue Count: 228 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ORPHAN NUCLEAR RECEPTOR NR1D1	C [auth A], D [auth B]	94	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20393 (Homo sapiens) Explore P20393  Go to UniProtKB:  P20393
PHAROS:  P20393 GTEx:  ENSG00000126368

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*(5IT)P*AP*GP*GP*TP*CP*AP*G)-3')	A [auth C]	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*G)-3')	B [auth D]	20	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.288 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.215 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.67	α = 75.16
b = 45.69	β = 80.64
c = 47.95	γ = 85.58

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-21 
Deposition Author(s): Zhao, Q., Khorasanizadeh, S., Rastinejad, F.

Revision History  

• Version 1.0: 1998-10-21
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Data collection, Database references, Derived calculations, Refinement description