PDBsum entry 2o4j

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Hormone/growth factor receptor PDB id
Jmol PyMol
Protein chains
240 a.a. *
12 a.a. *
Waters ×212
* Residue conservation analysis
PDB id:
Name: Hormone/growth factor receptor
Title: Crystal structure of rat vitamin d receptor ligand binding domain complexed with vitiii 17-20z and the nr2 box of drip 205
Structure: Vitamin d3 receptor. Chain: a. Fragment: ligand binding domain. Synonym: vdr, 1,25-dihydroxyvitamin d3 receptor. Engineered: yes. Mutation: yes. Peroxisome proliferator-activated receptor- binding protein. Chain: c.
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: vdr, nr1i1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthesized at uw-madison biotechnology center
1.74Å     R-factor:   0.201     R-free:   0.246
Authors: J.L.Vanhooke,M.M.Benning,H.F.Deluca
Key ref: J.L.Vanhooke et al. (2007). New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D3 with conformationally restricted side chains: evaluation of biological activity and structural determination of VDR-bound conformations. Arch Biochem Biophys, 460, 161-165. PubMed id: 17227670
04-Dec-06     Release date:   30-Jan-07    
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Protein chain
Pfam   ArchSchema ?
P13053  (VDR_RAT) -  Vitamin D3 receptor
423 a.a.
240 a.a.
Protein chain
Pfam   ArchSchema ?
Q15648  (MED1_HUMAN) -  Mediator of RNA polymerase II transcription subunit 1
1581 a.a.
12 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     steroid hormone mediated signaling pathway   2 terms 
  Biochemical function     DNA binding     3 terms  


Arch Biochem Biophys 460:161-165 (2007)
PubMed id: 17227670  
New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D3 with conformationally restricted side chains: evaluation of biological activity and structural determination of VDR-bound conformations.
J.L.Vanhooke, B.P.Tadi, M.M.Benning, L.A.Plum, H.F.DeLuca.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21119732 L.A.Plum, and H.F.DeLuca (2010).
Vitamin D, disease and therapeutic opportunities.
  Nat Rev Drug Discov, 9, 941-955.  
20535127 N.J.Nieves, J.M.Ahrens, L.A.Plum, H.F.DeLuca, and M.Clagett-Dame (2010).
Identification of a unique subset of 2-methylene-19-nor analogs of vitamin D with comedolytic activity in the rhino mouse.
  J Invest Dermatol, 130, 2359-2367.  
19183053 A.Teichert, L.A.Arnold, S.Otieno, Y.Oda, I.Augustinaite, T.R.Geistlinger, R.W.Kriwacki, R.K.Guy, and D.D.Bikle (2009).
Quantification of the vitamin D receptor-coregulator interaction.
  Biochemistry, 48, 1454-1461.  
19223058 T.Kaya, N.Swamy, K.S.Persons, S.Ray, S.C.Mohr, and R.Ray (2009).
Covalent labeling of nuclear vitamin D receptor with affinity labeling reagents containing a cross-linking probe at three different positions of the parent ligand: structural and biochemical implications.
  Bioorg Chem, 37, 57-63.  
19073913 G.D.Kutuzova, F.Sundersingh, J.Vaughan, B.P.Tadi, S.E.Ansay, S.Christakos, and H.F.Deluca (2008).
TRPV6 is not required for 1alpha,25-dihydroxyvitamin D3-induced intestinal calcium absorption in vivo.
  Proc Natl Acad Sci U S A, 105, 19655-19659.  
17904370 N.Yoshimoto, Y.Inaba, S.Yamada, M.Makishima, M.Shimizu, and K.Yamamoto (2008).
2-Methylene 19-nor-25-dehydro-1alpha-hydroxyvitamin D3 26,23-lactones: synthesis, biological activities and molecular basis of passive antagonism.
  Bioorg Med Chem, 16, 457-473.  
18384689 S.Ekins, E.J.Reschly, L.R.Hagey, and M.D.Krasowski (2008).
Evolution of pharmacologic specificity in the pregnane X receptor.
  BMC Evol Biol, 8, 103.  
17997857 E.J.Reschly, A.C.Bainy, J.J.Mattos, L.R.Hagey, N.Bahary, S.R.Mada, J.Ou, R.Venkataramanan, and M.D.Krasowski (2007).
Functional evolution of the vitamin D and pregnane X receptors.
  BMC Evol Biol, 7, 222.  
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