8P9W

vitamin D receptor complex with Xe4MeCF3 analog

• PDB DOI: https://doi.org/10.2210/pdb8P9W/pdb

• Classification: TRANSCRIPTION
• Organism(s): Danio rerio, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-06-06 Released: 2024-06-26 
• Deposition Author(s): Belorusova, A.Y., Rochel, N.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Literature

A vitamin D-based strategy overcomes chemoresistant prostate cancer

Belorusova, A.Y., Rochel, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 36.35 kDa 
• Atom Count: 2,061 
• Modelled Residue Count: 248 
• Deposited Residue Count: 317 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor A	A	302	Danio rerio	Mutation(s): 0  Gene Names: vdra, nr1i1a, vdr
UniProt
Find proteins for Q9PTN2 (Danio rerio) Explore Q9PTN2  Go to UniProtKB:  Q9PTN2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	B	15	Homo sapiens	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XDO (Subject of Investigation/LOI)	C [auth A]	(1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{S},3~{a}~{S},7~{a}~{S})-1,7~{a}-dimethyl-1-[6,6,6-tris(fluoranyl)-5-oxidanyl-5-(trifluoromethyl)hexa-1,3-diynyl]-2,3,3~{a},5,6,7-hexahydroinden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol C27 H30 F6 O3 MVLLQZOKYYYEBT-ZUDXOIQDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.82	α = 90
b = 65.82	β = 90
c = 263.22	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Belorusova, A.Y., Rochel, N.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release