9EZ2 | pdb_00009ez2

Vitamin D receptor complex with 1,4b,25-trihydroxyvitamin D3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.230 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1H72Click on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

4-Hydroxy-1 alpha ,25-Dihydroxyvitamin D 3 : Synthesis and Structure-Function Study.

Peluso-Iltis, C.Pierrat, N.Rovito, D.Osz, J.Sawada, D.Kittaka, A.Laverny, G.Rochel, N.

(2024) Biomolecules 14

  • DOI: https://doi.org/10.3390/biom14050551
  • Primary Citation of Related Structures:  
    9EZ1, 9EZ2

  • PubMed Abstract: 

    The active vitamin D metabolites, 25-hydroxyvitamin D 3 (25D 3 ) and 1,25-dihydroxyvitamin D 3 (1,25D 3 ), are produced by successive hydroxylation steps and play key roles in several cellular processes. However, alternative metabolic pathways exist, and among them, the 4-hydroxylation of 25D 3 is a major one. This study aims to investigate the structure-activity relationships of 4-hydroxy derivatives of 1,25D 3 . Structural analysis indicates that 1,4α,25(OH) 3 D 3 and 1,4β,25(OH) 3 D 3 maintain the anchoring hydrogen bonds of 1,25D 3 and form additional interactions, stabilizing the active conformation of VDR. In addition, 1,4α,25D 3 and 1,4β,25D 3 are as potent as 1,25D 3 in regulating the expression of VDR target genes in rat intestinal epithelial cells and in the mouse kidney. Moreover, these two 4-hydroxy derivatives promote hypercalcemia in mice at a dose similar to that of the parent compound.


  • Organizational Affiliation

    Institute of Genetics and Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin D3 receptor A302Danio rerioMutation(s): 0 
Gene Names: vdranr1i1avdr
UniProt
Find proteins for Q9PTN2 (Danio rerio)
Explore Q9PTN2 
Go to UniProtKB:  Q9PTN2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PTN2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 213Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.230 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.14α = 90
b = 66.14β = 90
c = 263.74γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1H72Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2024-06-19 
  • Deposition Author(s): Rochel, N.

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release