 |
PDBsum entry 1rgd
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
DNA binding protein
|
PDB id
|
|
|
|
1rgd
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structure refinement of the glucocorticoid receptor-Dna binding domain from nmr data by relaxation matrix calculations.
|
|
|
Authors
|
|
M.A.Van tilborg,
A.M.Bonvin,
K.Hård,
A.L.Davis,
B.Maler,
R.Boelens,
K.R.Yamamoto,
R.Kaptein.
|
|
|
Ref.
|
|
J Mol Biol, 1995,
247,
689-700.
|
|
|
PubMed id
|
|
|
|
|
Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
|
|
|
|
Abstract
|
|
|
The solution structure of the glucocorticoid receptor (GR) DNA-binding domain
(DBD), consisting of 93 residues, has been refined from two and
three-dimensional NMR data using an ensemble iterative relaxation matrix
approach followed by direct NOE refinement with DINOSAUR. A set of 47 structures
of the rat GR fragment Cys440-Arg510 was generated with distance geometry and
further refined with a combination of restrained energy minimization and
restrained molecular dynamics in a parallel refinement protocol. Distance
constraints were obtained from an extensive set of NOE build-up curves in H2O
and 2H2O via relaxation matrix calculations (1186 distance constraints from NOE
intensities, 10 phi and 22 chi 1 dihedral angle constraints from J- coupling
data were used for the calculations). The root-mean-square deviation values of
the 11 best structures on the well-determined part of the protein (Cys440 to
Ser448, His451 to Glu469 and Pro493 to Glu508) are 0.60 A and 1.20 A from the
average for backbone and all heavy atoms, respectively. The final structures
have R-factors around 0.40 and good stereochemical qualities. The first
zinc-coordinating domain of the GR DBD is very similar to the crystal structure
with a root-mean-square difference of 1.4 A. The second zinc-coordinating domain
is still disordered in solution. No secondary structure element is found in this
domain in the free state. As suggested by crystallographic studies on the
estrogen receptor DBD-DNA and GR DBD-DNA complexes, part of this region will
form a distorted helix and the D-box will undergo a conformational change upon
cooperative binding to DNA.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA.
|
|
|
Authors
|
|
B.F.Luisi,
W.X.Xu,
Z.Otwinowski,
L.P.Freedman,
K.R.Yamamoto,
P.B.Sigler.
|
|
|
Ref.
|
|
Nature, 1991,
352,
497-505.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Solution structure of the glucocorticoid receptor DNA-Binding domain.
|
|
|
Authors
|
|
T.Härd,
E.Kellenbach,
R.Boelens,
B.A.Maler,
K.Dahlman,
L.P.Freedman,
J.Carlstedt-Duke,
K.R.Yamamoto,
J.A.Gustafsson,
R.Kaptein.
|
|
|
Ref.
|
|
Science, 1990,
249,
157-160.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #3
|
|
|
Title
|
|
1h nmr studies of the glucocorticoid receptor DNA-Binding domain: sequential assignments and identification of secondary structure elements.
|
|
|
Authors
|
|
T.Härd,
E.Kellenbach,
R.Boelens,
R.Kaptein,
K.Dahlman,
J.Carlstedt-Duke,
L.P.Freedman,
B.A.Maler,
E.I.Hyde,
J.A.Gustafsson.
|
|
|
Ref.
|
|
Biochemistry, 1990,
29,
9015-9023.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
