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PDBsum entry 1kb2
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Transcription/DNA
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PDB id
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1kb2
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural basis of vdr-Dna interactions on direct repeat response elements.
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Authors
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P.L.Shaffer,
D.T.Gewirth.
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Ref.
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EMBO J, 2002,
21,
2242-2252.
[DOI no: ]
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PubMed id
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Abstract
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The vitamin D receptor (VDR) forms homo- or heterodimers on response elements
composed of two hexameric half-sites separated by 3 bp of spacer DNA. We
describe here the crystal structures at 2.7-2.8 A resolution of the VDR
DNA-binding region (DBD) in complex with response elements from three different
promoters: osteopontin (SPP), canonical DR3 and osteocalcin (OC). These
structures reveal the chemical basis for the increased affinity of VDR for the
SPP response element, and for the poor stability of the VDR-OC complex, relative
to the canonical DR3 response element. The homodimeric protein-protein interface
is stabilized by van der Waals interactions and is predominantly non-polar. An
extensive alpha-helix at the C-terminal end of the VDR DBD resembles that found
in the thyroid hormone receptor (TR), and suggests a mechanism by which VDR and
TR discriminate among response elements. Selective structure-based mutations in
the asymmetric homodimeric interface result in a VDR DBD protein that is
defective in homodimerization but now forms heterodimers with the 9-cis retinoic
acid receptor (RXR) DBD.
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Figure 1.
Figure 1 Protein and DNA constructs used in the structure
determination. (A) The human VDR DBD. Sequence numbers are for
full-length hVDR and those in parentheses refer to the common
hormone receptor DBD numbering scheme. Residues in italics are
disordered in all of the structures. (B) The 18 bp DNA duplexes
used in co-crystallization, shown 5'  arrow
3' in the top strand. Half-sites are shown in boxes and are
numbered by base pair. The DR3 sequence contains a direct repeat
of two consensus half-sites. SPP is the mouse osteopontin VDRE
and OC is the rat osteocalcin VDRE. Bases that differ from the
consensus sequence are shaded gray and the structurally
significant changes are highlighted in black. Estimates of
relative binding of VDR DBD homodimers to each sequence are also
shown.
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Figure 3.
Figure 3 Experimental electron density and homodimeric assembly.
(A) Unbiased experimental electron density from SAD phases. The
map is contoured around the CTE of the upstream subunit of the
VDR DBD−DR3 structure, which is shown as a C[  ]trace.
(B) A portion of the 2F[o] = F[c] electron density map showing
intersubunit dimerization contacts. (C) Stereo view of the
dimerization interface in a van der Waals surface
representation. (A) and (B) were made with Xtalview (McRee,
1999), and (C) was prepared with Ribbons.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
2242-2252)
copyright 2002.
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