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PDBsum entry 1ldp
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Complex (mhc i/peptide)
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PDB id
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1ldp
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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 2c tcr allorecognition of h-2ld peptide complexes.
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Authors
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J.A.Speir,
K.C.Garcia,
A.Brunmark,
M.Degano,
P.A.Peterson,
L.Teyton,
I.A.Wilson.
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Ref.
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Immunity, 1998,
8,
553-562.
[DOI no: ]
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PubMed id
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Abstract
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MHC class I H-2Ld complexed with peptide QL9 (or p2Ca) is a high-affinity
alloantigen for the 2C TCR. We used the crystal structure of H-2Ld with a
mixture of bound peptides at 3.1 A to construct a model of the allogeneic
2C-Ld/QL9 complex for comparison with the syngeneic 2C-Kb/dEV8 structure. A
prominent ridge on the floor of the Ld peptide-binding groove, not present in
Kb, creates a C-terminal bulge in Ld peptides that greatly increases
interactions with the 2C beta-chain. Furthermore, weak electrostatic
complementarity between Asp77 on the alpha1 helix of Kb and 2C is enhanced in
the allogeneic complex by closer proximity of QL9 peptide residue AspP8 to the
2C HV4 loop.
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Figure 1.
Figure 1. Ribbon Diagram of and Peptide Binding Groove
Electron Density in the H-2L^d Crystal Structure(A) Ribbon
diagram of the H-2L^d crystal structure viewed along the
peptide-binding groove. The peptide N-terminus is shown oriented
toward the viewer. (B) The peptide electron density in the
H-2L^d crystal structure. The σ[A]-weighted 2F[o]-F[c] electron
density is viewed with the peptide (APAAAAAAM) N-terminus on the
right to show the effect of the large polymorphic residues
(e.g., Trp73, Trp97, Tyr99) on the peptide conformation.
Residues below the peptide from three of the α[1]α[2] domain
β-strands and β[2]m (Trp60) form the bottom of the
peptide-binding groove. The map is contoured at 1.5σ with a
cover radius of 2.5 Å applied.
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Figure 2.
Figure 2. Structure Comparison of Selected Class I
MHC-Bound PeptidesThe MHC allele and peptide sequence are given
above the corresponding model. The peptides were superimposed
(bottom) by aligning only the α[1]α[2] C^α atoms of the MHC
molecules. The L^d tube diameter is enlarged in this
superimposition for clarity. The K^b peptide (dEV8) is one
residue shorter (P1–P8) than the others (P1–P9).
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The above figures are
reprinted
by permission from Cell Press:
Immunity
(1998,
8,
553-562)
copyright 1998.
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Secondary reference #1
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Title
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Structural basis of plasticity in t cell receptor recognition of a self peptide-Mhc antigen.
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Authors
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K.C.Garcia,
M.Degano,
L.R.Pease,
M.Huang,
P.A.Peterson,
L.Teyton,
I.A.Wilson.
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Ref.
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Science, 1998,
279,
1166-1172.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Structure of the 2C-H-2Kb-dEV8 complex. (A) Overall
backbone structure of one entire TCR-pMHC complex [only one of^
the two complexes in the asymmetric unit of the crystal is shown
(26)]. The TCR is on top (  chain
pink,  chain
light blue, CDR1[  ]magenta,
CDR2[ ]purple,
CDR3[ ]yellow,
CDR1[  ]cyan,
CDR2[ ]navy
blue, CDR3[ ]green,
HV4 orange). The pMHC^ is on the bottom (MHC heavy chain is
green, [2]-microglobulin
( [2]M) is
dark green, peptide is yellow with side chains shown). (B)
Close-up of the TCR-pMHC interface showing all side chains
involved^ in intermolecular contacts, and hydrogen bonds are
indicated. (C) Molecular surfaces of the interacting TCR,
peptide, and MHC with backbones and side chains visible through
the transparent surface. All figures were produced with Advanced
Visual System (AVS) software, and surfaces were calculated with
PQMS (25).
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Figure 3.
Fig. 3. Peptide-TCR interactions in the TCR-pMHC interface.
In the left two panels, a stereo pair of the backbone and side
chains of the TCR-pMHC interface are shown emphasizing the 2C
interactions with the NH[2]-terminal P1 (A), middle P4 (B), and^
COOH-terminal P6-P7 (C) positions of the bound dEV8 peptide. In
the companion panels to the far right, sliced molecular surfaces
of the region shown in the left panels highlight the relatively
poor complementarity of the peptide-TCR interaction. Large empty
gaps in the TCR-pMHC interface are evident in the molecular
surface^ representations. The TCR is shown in pink, the MHC in
green, the^ peptide in yellow, and water molecules in blue.
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The above figures are
reproduced from the cited reference
with permission from the AAAs
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