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PDBsum entry 1d9k
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Immune system
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PDB id
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1d9k
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Contents |
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110 a.a.
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112 a.a.
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183 a.a.
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188 a.a.
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16 a.a.
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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 crystal structure of a t cell receptor in complex with peptide and mhc class ii.
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Authors
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E.L.Reinherz,
K.Tan,
L.Tang,
P.Kern,
J.Liu,
Y.Xiong,
R.E.Hussey,
A.Smolyar,
B.Hare,
R.Zhang,
A.Joachimiak,
H.C.Chang,
G.Wagner,
J.Wang.
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Ref.
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Science, 1999,
286,
1913-1921.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of a complex involving the D10 T cell receptor (TCR),
16-residue foreign peptide antigen, and the I-Ak self major histocompatibility
complex (MHC) class II molecule is reported at 3.2 angstrom resolution. The D10
TCR is oriented in an orthogonal mode relative to its peptide-MHC (pMHC) ligand,
necessitated by the amino-terminal extension of peptide residues projecting from
the MHC class II antigen-binding groove as part of a mini beta sheet.
Consequently, the disposition of D10 complementarity-determining region loops is
altered relative to that of most pMHCI-specific TCRs; the latter TCRs assume a
diagonal orientation, although with substantial variability. Peptide
recognition, which involves P-1 to P8 residues, is dominated by the Valpha
domain, which also binds to the class II MHC beta1 helix. That docking is
limited to one segment of MHC-bound peptide offers an explanation for epitope
recognition and altered peptide ligand effects, suggests a structural basis for
alloreactivity, and illustrates how bacterial superantigens can span the
TCR-pMHCII surface.
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Figure 4.
Fig. 4. The high point "ridge" in pMHCII ligands is created, in
part, by the peptide. (A) Hydrogen bond network between the CA
peptide and I-A^k. The 10 hydrogen bonds between the CA and
I-A^k are shown as magenta dashed lines. These bonds are
conserved in known pMHCII structures. The helical regions from
I-A^k (colors as in Fig. 3) are shown as a backbone worm diagram
with those side chains and main-chain atoms involved in the
interactions displayed. The H2  1 helix
and H2a and H2b  1 helices
are labeled. (B) Stereo view of the molecular surface of I-A^k (
1 1) together
with the CA peptide (red), showing the surface topology of the
D10 docking platform on the CA/I-A^k ligand. (C) Stereo view of
the molecular surface of H-2Kb ( 1/ 2)
together with the dEV8 peptide (red) (6, 7) in the same view as
in (B), showing the smaller high point on the left side of the
docking platform for the MHC class I-restricted TCR molecule.
The peptide is mostly buried and makes little, if any,
contribution to the elevated points. Those residues contributing
to the high points of the platform are labeled in cyan in (B)
and (C).
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Figure 6.
Fig. 6. Model of the scD10-SEB-pMHCII interaction complex. (A)
Superposition of the V C -SEB
complex (in dark blue) and the scD10-CA/I-A^k complex. The V
domains
from each complex were used for least-square fitting (92 C atoms from
residues Val3-Gly94 of V , rmsd =
0.67 Å). The color scheme for the complex of D10-CA/I-A^k
is as labeled. (B) The superposition of the SEB/HLA-DR1 complex
(in brown) to the already superimposed V C -SEB
complex (in dark blue) and scD10 (V V ) module
derived from (A). The two SEB superantigen molecules were used
for least-square fitting (83 C atoms,
rmsd = 0.63 Å). (C) scD10-SEB-CA/I-A^k interaction
complex. DR1 in Fig. 6B has been replaced with I-A^k on the
basis of structural alignment of residues of the two helices of
each MHC molecule (43 C atoms,
rmsd = 1.02 Å).
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The above figures are
reprinted
by permission from the AAAs:
Science
(1999,
286,
1913-1921)
copyright 1999.
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