5V39

Crystal structure of human vitamin D receptor ligand binding domain in complex with a VDRM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

HDX reveals the conformational dynamics of DNA sequence specific VDR co-activator interactions.

Zheng, J.Chang, M.R.Stites, R.E.Wang, Y.Bruning, J.B.Pascal, B.D.Novick, S.J.Garcia-Ordonez, R.D.Stayrook, K.R.Chalmers, M.J.Dodge, J.A.Griffin, P.R.

(2017) Nat Commun 8: 923-923

  • DOI: 10.1038/s41467-017-00978-7

  • PubMed Abstract: 
  • The vitamin D receptor/retinoid X receptor-α heterodimer (VDRRXRα) regulates bone mineralization via transcriptional control of osteocalcin (BGLAP) gene and is the receptor for 1α,25-dihydroxyvitamin D <sub>3 </sub> (1,25D3). However, supra-physiolog ...

    The vitamin D receptor/retinoid X receptor-α heterodimer (VDRRXRα) regulates bone mineralization via transcriptional control of osteocalcin (BGLAP) gene and is the receptor for 1α,25-dihydroxyvitamin D 3 (1,25D3). However, supra-physiological levels of 1,25D3 activates the calcium-regulating gene TRPV6 leading to hypercalcemia. An approach to attenuate this adverse effect is to develop selective VDR modulators (VDRMs) that differentially activate BGLAP but not TRPV6. Here we present structural insight for the action of a VDRM compared with agonists by employing hydrogen/deuterium exchange. Agonist binding directs crosstalk between co-receptors upon DNA binding, stabilizing the activation function 2 (AF2) surfaces of both receptors driving steroid receptor co-activator-1 (SRC1) interaction. In contrast, AF2 of VDR within VDRM:BGLAP bound heterodimer is more vulnerable for large stabilization upon SRC1 interaction compared with VDRM:TRPV6 bound heterodimer. These results reveal that the combination of ligand structure and DNA sequence tailor the transcriptional activity of VDR toward specific target genes.The vitamin D receptor/retinoid X receptor-α heterodimer (VDRRXRα) regulates bone mineralization. Here the authors employ hydrogen/deuterium exchange (HDX) mass spectrometry to study the conformational dynamics of VDRRXRα and give mechanistic insights into how VDRRXRα controls the transcriptional activity of specific genes.


    Organizational Affiliation

    Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA. pgriffin@scripps.edu.,Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, 46225, USA.,The University of Adelaide, Institute for Photonics & Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
257Homo sapiensMutation(s): 0 
Gene Names: VDR (NR1I1)
Find proteins for P11473 (Homo sapiens)
Go to Gene View: VDR
Go to UniProtKB:  P11473
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8VM
Query on 8VM

Download SDF File 
Download CCD File 
A
5-(3-{4-[(2S)-2-hydroxy-3,3-dimethylbutoxy]-3-methylphenyl}pentan-3-yl)-3-methyl-N-(1H-tetrazol-5-yl)thiophene-2-carboxamide
C25 H35 N5 O3 S
XZOVDHKWBOZRPS-LJQANCHMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.000α = 90.00
b = 52.670β = 90.00
c = 105.880γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2019-04-03
    Type: Data collection, Database references