6T2M | pdb_00006t2m

VDR-ZK168281 complex

• PDB DOI: https://doi.org/10.2210/pdb6T2M/pdb

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


• Deposited: 2019-10-09 Released: 2020-08-26 
• Deposition Author(s): Rochel, N., Belorusova, A.Y.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structural Analysis of VDR Complex with ZK168281 Antagonist.

Belorusova, A.Y., Chalhoub, S., Rovito, D., Rochel, N.

(2020) J Med Chem 63: 9457-9463

• PubMed: 32787090 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c00656
• Primary Citation of Related Structures:  
  6T2M


• PubMed Abstract: 
  

  Vitamin D receptor (VDR) antagonists prevent the VDR activation function helix 12 from folding into its active conformation, thus affecting coactivator recruitment and antagonizing the transcriptional regulation induced by 1α,25-dihydroxyvitamin D3. Here, we report the crystal structure of the zebrafish VDR ligand-binding domain in complex with the ZK168281 antagonist, revealing that the ligand prevents optimal folding of the C-terminal region of VDR. This interference was confirmed by hydrogen-deuterium exchange mass spectrometry (HDX-MS) in solution.

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Organizational Affiliation: 

Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France.

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 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 36.35 kDa 
• Atom Count: 2,049 
• Modelled Residue Count: 249 
• 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
M9Q (Subject of Investigation/LOI)	C [auth A]	ethyl (~{Z})-3-[1-[(~{E},1~{R},4~{R})-4-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[(2~{Z})-2-[(3~{S},5~{R})-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-oxidanyl-pent-2-enyl]cyclopropyl]prop-2-enoate C32 H46 O5 FUDAEUIGIJZUAY-MRFCKDSNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.155	α = 90
b = 66.155	β = 90
c = 265.315	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Rochel, N., Belorusova, A.Y.

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Funding Organization	Location	Grant Number
French National Research Agency	France	--

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 1.2: 2021-02-24
  Changes: Derived calculations
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description