2NLL

RETINOID X RECEPTOR-THYROID HORMONE RECEPTOR DNA-BINDING DOMAIN HETERODIMER BOUND TO THYROID RESPONSE ELEMENT DNA

• PDB DOI: https://doi.org/10.2210/pdb2NLL/pdb
• NAKB: 2NLL

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


• Deposited: 1996-11-20 Released: 1997-03-12 
• Deposition Author(s): Rastinejad, F., Perlmann, T., Evans, R.M., Sigler, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.269 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Literature

Structural determinants of nuclear receptor assembly on DNA direct repeats.

Rastinejad, F., Perlmann, T., Evans, R.M., Sigler, P.B.

(1995) Nature 375: 203-211

• PubMed: 7746322 
• DOI: https://doi.org/10.1038/375203a0
• Primary Citation of Related Structures:  
  2NLL


• PubMed Abstract: 
  

  Nuclear receptor heterodimers recognize response elements composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs. The 1.9 A crystal structure of the complex formed by the DNA-binding domains of the 9-cis retinoic acid receptor and thyroid hormone receptor bound to a thyroid-response element shows that the subunits interact through a DNA-supported interface involving the carboxy-terminal extension of the DNA-binding domain of the thyroid hormone receptor. The stereochemistry suggests a mechanism by which heterodimers recognize the inter-half-site spacing between direct repeats.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.36 kDa 
• Atom Count: 2,351 
• Modelled Residue Count: 205 
• Deposited Residue Count: 205 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (RETINOIC ACID RECEPTOR)	C [auth A]	66	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens) Explore P19793  Go to UniProtKB:  P19793
PHAROS:  P19793 GTEx:  ENSG00000186350

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (THYROID HORMONE RECEPTOR)	D [auth B]	103	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10828 (Homo sapiens) Explore P10828  Go to UniProtKB:  P10828
PHAROS:  P10828 GTEx:  ENSG00000151090

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*TP*TP*(5IU)P*CP*AP*GP*GP*TP*CP*AP*G)-3')	A [auth C]	18	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*GP*AP*AP*AP*TP*GP*AP*CP*CP*T P*G)-3')	B [auth D]	18	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: 1.90 Å
• R-Value Free: 0.269 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.9	α = 90
b = 65.6	β = 90
c = 125.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-03-12 
Deposition Author(s): Rastinejad, F., Perlmann, T., Evans, R.M., Sigler, P.B.

Revision History  

• Version 1.0: 1997-03-12
  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: 2024-02-21
  Changes: Data collection, Database references, Derived calculations