Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34969.25 
• Atom Count: 2030 
• Residue Count: 305 
• Unique protein chains: 2

2O4J

Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20Z and the NR2 Box of DRIP 205

• DOI: 10.2210/pdb2O4J/pdb

• Classification: HORMONE/GROWTH FACTOR RECEPTOR
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli


• Deposited: 2006-12-04 Released: 2007-01-30 
• Deposition Author(s): Vanhooke, J.L., Benning, M.M., DeLuca, H.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 

Literature

New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D(3) with conformationally restricted side chains: Evaluation of biological activity and structural determination of VDR-bound conformations.

Vanhooke, J.L., Tadi, B.P., Benning, M.M., Plum, L.A., Deluca, H.F.

(2007) Arch.Biochem.Biophys. 460: 161-165

• PubMed: 17227670 
• DOI: 10.1016/j.abb.2006.11.029
• Primary Citation of Related Structures:  
  2O4R


• PubMed Abstract: 
  

We have successfully prepared E- and Z- isomers of 17-20 dehydro analogs of 2-methylene-19-nor-(20S)-1alpha,25-dihydroxyvitamin D3 (2MD). Both isomers bind to the recombinant rat vitamin D receptor (VDR) with high affinity. The Z-isomer (Vit-III 17-20Z) displays activity in vivo and in vitro that is similar to 2MD. The in vitro activity of the E-isomer (Vit-III 17-20E) is comparable to the natural hormone, though in vivo this analog is significantly less calcemic. Crystal structures of the rat VDR ligand binding domain complexed with the analogs demonstrate that the Vit-III 17-20Z analog is oriented almost identically to 2MD, with only minor differences induced by the planar configuration around the C17-C20 double bond. The Vit-III 17-20E analog is oriented in a conformation distinct from both 2MD and the natural hormone. The structural comparisons suggest that the position of C21 in the ligand binding site may be an important determinant of biological activity.

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Related Citations: 

• Molecular Structure of the Rat Vitamin D Receptor Ligand Binding Domain Complexed with 2-Carbon-Substituted Vitamin D3 Hormone Analogues and a LXXLL-Containing Coactivator Peptide
  Vanhooke, J.L.,Benning, M.M.,Bauer, C.B.,Pike, J.W.,DeLuca, H.F.
  (2004) Biochemistry 43: 4101




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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Vitamin D3 receptor	A	292	Rattus norvegicus	Mutation(s): 0  Gene Names: Vdr (Nr1i1)
Find proteins for P13053 (Rattus norvegicus) Go to UniProtKB:  P13053

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Peroxisome proliferator-activated receptor-binding protein	C	13	Homo sapiens	Mutation(s): 0  Gene Names: MED1 (ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2)
Find proteins for Q15648 (Homo sapiens) Go to Gene View: MED1 Go to UniProtKB:  Q15648

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
VD4	A	(1R,3R,7E,17Z)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra-5,7-diene-1,3-diol C27 H42 O3 PCPYFQNISYYIPU-DUKKOGHCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
VD4	Ki: 0.08 nM BINDINGMOAD
VD4	Ki: 0.08 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 155.500	α = 90.00
b = 42.400	β = 96.50
c = 41.900	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
LSCALE	data scaling
PDB_EXTRACT	data extraction
SAINT	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-12-04 
• Released Date: 2007-01-30 
• Deposition Author(s): Vanhooke, J.L., Benning, M.M., DeLuca, H.F.

Revision History 

• Version 1.0: 2007-01-30
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-18
  Type: Refinement description