Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 32638.68 
• Atom Count: 2076 
• Residue Count: 284 
• Unique protein chains: 2

3WT6

A mixed population of antagonist and agonist binding conformers in a single crystal explains partial agonism against vitamin D receptor: Active vitamin D analogues with 22R-alkyl group

• DOI: 10.2210/pdb3WT6/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli


• Deposited: 2014-04-08 Released: 2014-06-11 
• Deposition Author(s): Anami, Y., Itoh, T., Yamamoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.224 
• R-Value Work: 0.199 

Literature

A Mixed Population of Antagonist and Agonist Binding Conformers in a Single Crystal Explains Partial Agonism against Vitamin D Receptor: Active Vitamin D Analogues with 22R-Alkyl Group.

Anami, Y., Itoh, T., Egawa, D., Yoshimoto, N., Yamamoto, K.

(2014) J.Med.Chem. 57: 4351-4367

• PubMed: 24742174 
• DOI: 10.1021/jm500392t
• Primary Citation of Related Structures:  
  3WT7, 3WT5


• PubMed Abstract: 
  

We are continuing to study the structural basis of vitamin D receptor (VDR) agonism and antagonism by using 22S-alkyl vitamin D analogues. Here we report the synthesis and biological evaluation of 22R-alkyl analogues and the X-ray crystallographic analysis of vitamin D receptor ligand-binding domain (VDR-LBD) complexed with a 22R-analogue. VDR-LBD complexed with the partial agonist 8a showed that 8a binds to VDR-LBD with two conformations, one of which is the antagonist/VDR-LBD complex structure and the other is the agonist/VDR-LBD complex structure. The results indicate that the partial agonist activity of 8a depends on the sum of antagonistic and agonistic activities caused by the antagonist and agonist binding conformers, respectively. The structural basis observed here must be applicable to the partial agonism of other ligand-dependent nuclear receptors. This is the first report describing the trapping of a conformational subset of the ligand and the nuclear receptor in a single crystal.

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Organizational Affiliation: 

Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Vitamin D3 receptor	A	271	Rattus norvegicus	Mutation(s): 0  Gene Names: Vdr (Nr1i1)
Find proteins for P13053 (Rattus norvegicus) Go to UniProtKB:  P13053

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Mediator of RNA polymerase II transcription subunit 1	C	13	Homo sapiens	Mutation(s): 0  Gene Names: MED1 (ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2)
Find proteins for Q15648 (Homo sapiens) Go to Gene View: MED1 Go to UniProtKB:  Q15648

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
YA1	A	(1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol C31 H52 O3 RSXHMKSDJHHTDU-PJSVQGINSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
YA1	IC50: 0.29 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.224 
• R-Value Work: 0.199 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 127.050	α = 90.00
b = 44.770	β = 94.20
c = 45.110	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SERGUI	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-04-08 
• Released Date: 2014-06-11 
• Deposition Author(s): Anami, Y., Itoh, T., Yamamoto, K.

Revision History 

• Version 1.0: 2014-06-11
  Type: Initial release
• Version 1.1: 2017-11-22
  Type: Refinement description