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DNA-binding receptor
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PDB id
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1hra
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Contents |
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* Residue conservation analysis
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Gene Ontology (GO) functional annotation
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Cellular component
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nucleus
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1 term
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Biological process
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regulation of transcription, DNA-dependent
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1 term
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Biochemical function
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DNA binding
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6 terms
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DOI no:
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J Biomol Nmr
3:1
(1993)
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PubMed id:
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The solution structure of the human retinoic acid receptor-beta DNA-binding domain.
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R.M.Knegtel,
M.Katahira,
J.G.Schilthuis,
A.M.Bonvin,
R.Boelens,
D.Eib,
P.T.van der Saag,
R.Kaptein.
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ABSTRACT
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The three-dimensional structure of the DNA-binding domain of the human retinoic
acid receptor-beta (hRAR-beta) has been determined by nuclear magnetic resonance
spectroscopy in conjunction with distance geometry, restrained molecular
dynamics and iterative relaxation matrix calculations. A total of 1244 distance
restraints were obtained from NOE intensities, of which 448 were intra-residue
and 796 inter-residue restraints. In addition 23 chi and 30 phi dihedral angle
restraints were obtained from J-coupling data. The two 'zinc-finger' regions of
the 80-amino acid residue protein are followed by two alpha-helices that cross
each other perpendicularly. There is a short stretch of b-sheet near the
N-terminus. The alpha-helical core of the protein is well determined with a
backbone root-mean-square deviation (r.m.s.d.) with respect to the average of
0.18 A and 0.37 A when the side chains of residues 31, 32, 36, 61, 62, 65 and 69
are included. The r.m.s.d. for the backbone of residues 5-80 is 0.76 A. For the
first finger (residues 8-28), the r.m.s.d. of the backbone is 0.79 A. For the
second finger (residues 44-62) the r.m.s.d. is 0.64 A. The overall structure is
similar to that of the corresponding domain of the glucocorticoid receptor,
although the C-terminal part of the protein is different. The second alpha-helix
is two residues shorter and is followed by a well-defined region of extended
backbone structure.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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F.Rastinejad,
T.Wagner,
Q.Zhao,
and
S.Khorasanizadeh
(2000).
Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1.
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EMBO J, 19,
1045-1054.
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PDB code:
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P.J.van Tilborg,
M.Czisch,
F.A.Mulder,
G.E.Folkers,
A.M.Bonvin,
M.Nair,
R.Boelens,
and
R.Kaptein
(2000).
Changes in dynamical behavior of the retinoid X receptor DNA-binding domain upon binding to a 14 base-pair DNA half site.
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Biochemistry, 39,
8747-8757.
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D.S.Sem,
D.R.Casimiro,
S.A.Kliewer,
J.Provencal,
R.M.Evans,
and
P.E.Wright
(1997).
NMR spectroscopic studies of the DNA-binding domain of the monomer-binding nuclear orphan receptor, human estrogen related receptor-2. The carboxyl-terminal extension to the zinc-finger region is unstructured in the free form of the protein.
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J Biol Chem, 272,
18038-18043.
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C.Rachez,
P.Sautière,
P.Formstecher,
and
P.Lefebvre
(1996).
Identification of amino acids critical for the DNA binding and dimerization properties of the human retinoic acid receptor alpha. Importance of lysine 360, lysine 365, and valine 361.
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J Biol Chem, 271,
17996-18006.
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J.A.Lupisella,
J.E.Driscoll,
W.J.Metzler,
and
P.R.Reczek
(1995).
The ligand binding domain of the human retinoic acid receptor gamma is predominantly alpha-helical with a Trp residue in the ligand binding site.
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J Biol Chem, 270,
24884-24890.
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J.W.Schwabe,
L.Chapman,
and
D.Rhodes
(1995).
The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation.
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Structure, 3,
201-213.
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L.D.McBroom,
G.Flock,
and
V.Giguère
(1995).
The nonconserved hinge region and distinct amino-terminal domains of the ROR alpha orphan nuclear receptor isoforms are required for proper DNA bending and ROR alpha-DNA interactions.
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Mol Cell Biol, 15,
796-808.
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G.J.Kleywegt,
T.Bergfors,
H.Senn,
P.Le Motte,
B.Gsell,
K.Shudo,
and
T.A.Jones
(1994).
Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid.
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Structure, 2,
1241-1258.
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PDB codes:
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J.Zilliacus,
J.Carlstedt-Duke,
J.A.Gustafsson,
and
A.P.Wright
(1994).
Evolution of distinct DNA-binding specificities within the nuclear receptor family of transcription factors.
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Proc Natl Acad Sci U S A, 91,
4175-4179.
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M.S.Lee,
D.S.Sem,
S.A.Kliewer,
J.Provencal,
R.M.Evans,
and
P.E.Wright
(1994).
NMR assignments and secondary structure of the retinoid X receptor alpha DNA-binding domain. Evidence for the novel C-terminal helix.
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Eur J Biochem, 224,
639-650.
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J.W.Schwabe,
L.Chapman,
J.T.Finch,
D.Rhodes,
and
D.Neuhaus
(1993).
DNA recognition by the oestrogen receptor: from solution to the crystal.
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Structure, 1,
187-204.
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
