1rkh: Difference between revisions
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[[Image:1rkh.gif|left|200px]] | [[Image:1rkh.gif|left|200px]] | ||
'''crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2AM20R and a synthetic peptide containing the NR2 box of DRIP 205''' | {{Structure | ||
|PDB= 1rkh |SIZE=350|CAPTION= <scene name='initialview01'>1rkh</scene>, resolution 2.28Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=VD2:5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYL-CYCLOHEXANE-1,3-DIOL'>VD2</scene> | |||
|ACTIVITY= | |||
|GENE= VDR, NR1I1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus]) | |||
}} | |||
'''crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2AM20R and a synthetic peptide containing the NR2 box of DRIP 205''' | |||
==Overview== | ==Overview== | ||
| Line 10: | Line 19: | ||
==About this Structure== | ==About this Structure== | ||
1RKH is a [ | 1RKH is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKH OCA]. | ||
==Reference== | ==Reference== | ||
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 JL, Benning MM, Bauer CB, Pike JW, DeLuca HF, Biochemistry. 2004 Apr 13;43(14):4101-10. PMID:[http:// | 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 JL, Benning MM, Bauer CB, Pike JW, DeLuca HF, Biochemistry. 2004 Apr 13;43(14):4101-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15065852 15065852] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Rattus norvegicus]] | [[Category: Rattus norvegicus]] | ||
| Line 22: | Line 31: | ||
[[Category: Vanhooke, J L.]] | [[Category: Vanhooke, J L.]] | ||
[[Category: VD2]] | [[Category: VD2]] | ||
[[Category: nuclear receptor-coactivator | [[Category: nuclear receptor-coactivator interaction]] | ||
[[Category: nuclear receptor-ligand complex]] | [[Category: nuclear receptor-ligand complex]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:52:49 2008'' | ||
Revision as of 14:52, 20 March 2008
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| , resolution 2.28Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | VDR, NR1I1 (Rattus norvegicus) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2AM20R and a synthetic peptide containing the NR2 box of DRIP 205
OverviewOverview
We have determined the crystal structures of the ligand binding domain (LBD) of the rat vitamin D receptor in ternary complexes with a synthetic LXXLL-containing peptide and the following four ligands: 1alpha,25-dihydroxyvitamin D(3); 2-methylene-19-nor-(20S)-1alpha,25-dihydroxyvitamin D(3) (2MD); 1alpha-hydroxy-2-methylene-19-nor-(20S)-bishomopregnacalciferol (2MbisP), and 2alpha-methyl-19-nor-1alpha,25-dihydroxyvitamin D(3) (2AM20R). The conformation of the LBD is identical in each complex. Binding of the 2-carbon-modified analogues does not change the positions of the amino acids in the ligand binding site and has no effect on the interactions in the coactivator binding pocket. The CD ring of the superpotent analogue, 2MD, is tilted within the binding site relative to the other ligands in this study and to (20S)-1alpha,25-dihydroxyvitamin D(3) [Tocchini-Valentini et al. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 5491-5496]. The aliphatic side chain of 2MD follows a different path within the binding site; nevertheless, the 25-hydroxyl group at the end of the chain occupies the same position as that of the natural ligand, and the hydrogen bonds with histidines 301 and 393 are maintained. 2MbisP binds to the receptor despite the absence of the 25-hydroxyl group. A water molecule is observed between His 301 and His 393 in this structure, and it preserves the orientation of the histidines in the binding site. Although the alpha-chair conformer is highly favored in solution for the A ring of 2AM20R, the crystal structures demonstrate that this ring assumes the beta-chair conformation in all cases, and the 1alpha-hydroxyl group is equatorial. The peptide folds as a helix and is anchored through hydrogen bonds to a surface groove formed by helices 3, 4, and 12. Electrostatic and hydrophobic interactions between the peptide and the LBD stabilize the active receptor conformation. This stablization appears necessary for crystal growth.
DiseaseDisease
Known diseases associated with this structure: Joubert syndrome 5 OMIM:[610142], Leber congenital amaurosis, type X OMIM:[610142], Meckel syndrome type 4 OMIM:[610142], Senior-Loken syndrome 6 OMIM:[610142]
About this StructureAbout this Structure
1RKH is a Protein complex structure of sequences from Rattus norvegicus. Full crystallographic information is available from OCA.
ReferenceReference
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 JL, Benning MM, Bauer CB, Pike JW, DeLuca HF, Biochemistry. 2004 Apr 13;43(14):4101-10. PMID:15065852
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