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PDBsum entry 1j87
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Immune system
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PDB id
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1j87
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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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The analysis of the human high affinity ige receptor fc epsilon ri alpha from multiple crystal forms.
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Authors
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S.C.Garman,
S.Sechi,
J.P.Kinet,
T.S.Jardetzky.
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Ref.
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J Mol Biol, 2001,
311,
1049-1062.
[DOI no: ]
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PubMed id
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Abstract
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We have solved the structure of the human high affinity IgE receptor, Fc epsilon
RI alpha, in six different crystal forms, showing the structure in 15 different
chemical environments. This database of structures shows no change in the
overall shape of the molecule, as the angle between domains 1 and 2 (D1 and D2)
varies little across the ensemble. However, the receptor has local
conformational variability in the C' strand of D2 and in the BC loop of D1. In
every crystal form, a residue inserts between tryptophan residues 87 and 110,
mimicking the position of a proline from the IgE ligand. The different crystal
forms reveal a distribution of carbohydrates lining the front and back surfaces
of the structure. An analysis of crystal contacts in the different forms
indicates regions where the molecule interacts with other proteins, and reveals
a potential new binding site distal to the IgE binding site. The results of this
study point to new directions for the design of molecules to inhibit the
interaction of Fc epsilon RI alpha with its natural ligand and thus to prevent a
primary step in the allergic response.
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Figure 2.
Figure 2. Close-up of binding site 1 in eight different
structures. C^a positions for residues 125-138 are shown, along
with side-chain atoms for residues Tyr129, Trp130, and Tyr131.
(a) Chains are colored according to the scheme in Figure 1: form
M1, white; form M2 (copy A), green; form M2 (copy B), yellow;
form H1, blue; form Complex1, cyan; form T1 (copies A and B),
red; form T2 (copy A), magenta. Other copies of the tetragonal
forms are identical; only one representative structure is shown.
In form M1, form M2A, and form H1, the coordinates differ from
canonical C' structure. (b) The same Figure is shown with a
different coloring scheme, showing the variation in location of
three aromatic residues. Side-chain atoms for Tyr129 appear red,
for Trp130 appear blue, and for Tyr131 appear yellow. Tyr131 in
form M2A falls in nearly the same location as Tyr129 in most
crystal forms.
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Figure 3.
Figure 3. Electron density from four structures. Electron
density maps were calculated using s[a]-weighted simulated
annealing composite omit map protocols in the program CNS. Atoms
are drawn from residue 125 to 134, near binding site 1 in domain
D2, and the maps are drawn around the atoms. (a) Form M1. The
2.4 Å map is contoured at 1.2s. The strand is in a
location intermediate between C' and D strands. (b) Form M2,
copy A. The 3.2 Å map is contoured at 1.2s. The atoms form
a single turn of a-helix surrounded by random coil and are in
found in an intermediate location between C' and D strands. (c)
Form H1. The 3.2 Å map is contoured at 0.9s. The atoms
have crossed over to the opposite sheet of the Ig domain; they
form b strand D hydrogen-bonded to the E strand. (d) Form M2,
copy B. The 3.2 Å map is contoured at 1.2s. This is the
most common conformation for the Fc  epsilon
RIa chain, a C' strand hydrogen-bonded to the C strand in D2,
seen in 12 of the 15 structures.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
311,
1049-1062)
copyright 2001.
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