5H1E

Interaction between vitamin D receptor and coactivator peptide SRC2-3

• PDB DOI: https://doi.org/10.2210/pdb5H1E/pdb

• Classification: TRANSCRIPTION
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-08 Released: 2017-01-11 
• Deposition Author(s): Egawa, D., Itoh, T., Kato, A., Kataoka, S., Anami, Y., Yamamoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.248 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

SRC2-3 binds to vitamin D receptor with high sensitivity and strong affinity

Egawa, D., Itoh, T., Kato, A., Kataoka, S., Anami, Y., Yamamoto, K.

(2017) Bioorg Med Chem 25: 568-574

• PubMed: 27890450 
• DOI: https://doi.org/10.1016/j.bmc.2016.11.020
• Primary Citation of Related Structures:  
  5H1E


• PubMed Abstract: 
  

  Vitamin D receptor (VDR) is a member of the nuclear receptor superfamily and regulates the expression of target genes through ligand binding. To express the target gene, coactivator binding to the VDR/ligand complex is essential. Although there are many coactivators in living cells, precise interactions between coactivators and VDR have not been clarified. Here, we synthesized two coactivator peptides, DRIP205-2 and SRC2-3, evaluated their affinity for the ligand-binding domain (LBD) of VDR using 1α,25-dihydroxyvitamin D ₃ , partial agonist 1, and antagonist 2 by surface plasmon resonance (SPR), and assessed their interaction modes with VDR-LBD using X-ray crystallographic analysis. This study showed that the SRC2-3 peptide is more sensitive to the ligands (agonist, partial agonist, and antagonist) and shows more intimate interactions with VDR-LBD than DRIP205-2 peptide.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 32.61 kDa 
• Atom Count: 2,081 
• Modelled Residue Count: 249 
• Deposited Residue Count: 284 
• Unique protein chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2 peptide	B [auth C]	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VDX	C [auth A]	5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL C27 H44 O3 GMRQFYUYWCNGIN-NKMMMXOESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.248 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.77	α = 90
b = 42.88	β = 95.83
c = 42.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Egawa, D., Itoh, T., Kato, A., Kataoka, S., Anami, Y., Yamamoto, K.

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references