3W0G

Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands

• PDB DOI: https://doi.org/10.2210/pdb3W0G/pdb

• Classification: TRANSCRIPTION
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-30 Released: 2013-10-09 
• Deposition Author(s): Shimizu, T., Asano, L., Kuwabara, N., Ito, I., Waku, T., Yanagisawa, J., Miyachi, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.258 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Starting Model: experimental

Literature

Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands.

Asano, L., Ito, I., Kuwabara, N., Waku, T., Yanagisawa, J., Miyachi, H., Shimizu, T.

(2013) FEBS Lett 587: 957-963

• PubMed: 23462137 
• DOI: https://doi.org/10.1016/j.febslet.2013.02.028
• Primary Citation of Related Structures:  
  3W0G, 3W0H, 3W0I, 3W0J


• PubMed Abstract: 
  

  Non-secosteroidal ligands for vitamin D receptor (VDR) have been developed for the agonist with non-calcemic profiles. Here, we provide the structural mechanism of VDR agonism by novel non-secosteroidal ligands. All ligands had the similar efficacy, while two had the higher potency. Crystallographic analyses revealed that all ligands interacted with helix H10 and the loop between helices H6 and H7 in a similar manner, but also that the two ligands with higher potency had different interaction modes. This study suggests that distinct ligand potency depend upon differences in the formation and rearrangement of hydrogen-bond networks induced by each ligand.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.73 kDa 
• Atom Count: 2,198 
• Modelled Residue Count: 254 
• Deposited Residue Count: 266 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	253	Rattus norvegicus	Mutation(s): 0  Gene Names: Nr1i1, Vdr
UniProt
Find proteins for P13053 (Rattus norvegicus) Explore P13053  Go to UniProtKB:  P13053

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 1	B [auth C]	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15648 (Homo sapiens) Explore Q15648  Go to UniProtKB:  Q15648
PHAROS:  Q15648 GTEx:  ENSG00000125686

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W07	C [auth A]	(2S)-3-{4-[2-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}phenyl)propan-2-yl]phenoxy}propane-1,2-diol C24 H34 O5 NSXHQTLHHLJUGK-UGKGYDQZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.258 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.303	α = 90
b = 41.975	β = 94.86
c = 42.05	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Shimizu, T., Asano, L., Kuwabara, N., Ito, I., Waku, T., Yanagisawa, J., Miyachi, H.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description