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* Residue conservation analysis
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DOI no:
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Proc Natl Acad Sci U S A
92:2479-2483
(1995)
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PubMed id:
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Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove.
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D.H.Fremont,
E.A.Stura,
M.Matsumura,
P.A.Peterson,
I.A.Wilson.
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ABSTRACT
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Sequence analysis of peptides naturally presented by major histocompatibility
complex (MHC) class I molecules has revealed allele-specific motifs in which the
peptide length and the residues observed at certain positions are restricted.
Nevertheless, peptides containing the standard motif often fail to bind with
high affinity or form physiologically stable complexes. Here we present the
crystal structure of a well-characterized antigenic peptide from ovalbumin
in complex with the murine MHC class I
H-2Kb molecule at 2.5-A resolution. Hydrophobic peptide residues Ile-P2 and
Phe-P5 are packed closely together into binding pockets B and C, suggesting that
the interplay of peptide anchor (P5) and secondary anchor (P2) residues can
couple the preferred sequences at these positions. Comparison with the crystal
structures of H-2Kb in complex with peptides VSV-8 (RGYVYQGL) and SEV-9
(FAPGNYPAL), where a Tyr residue is used as the C pocket anchor, reveals that
the conserved water molecule that binds into the B pocket and mediates hydrogen
bonding from the buried anchor hydroxyl group could not be likewise positioned
if the P2 side chain were of significant size. Based on this structural
evidence, H-2Kb has at least two submotifs: one with Tyr at P5 (or P6 for
nonamer peptides) and a small residue at P2 (i.e., Ala or Gly) and another with
Phe at P5 and a medium-sized hydrophobic residue at P2 (i.e., Ile). Deciphering
of these secondary submotifs from both crystallographic and immunological
studies of MHC peptide binding should increase the accuracy of T-cell epitope
prediction.
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Selected figure(s)
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Figure 1.
FIG. 1. Fo-Fc omit electron density map of OVA-8 (SIINFEKL)
bound to H-2Kb at 2.5-A resolution contoured at 2.5 ur.
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Figure 3.
FIG. 3. OVA-8-associated conformational differences in H-2Kb.
The N-terminal regions of OVA-8 (magenta), VSV-8 (yellow), and
SEV-9 (cyan) complexes are rendered as tubes. majority of MHC
I-peptide interactions are conserved in all three but
nevertheless slight variations in the conformation of Glu-63,
and especially Trp-167 are observed that apparently result from the
differences in the sequences of the bound peptides.
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Figures were
selected
by an automated process.
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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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PDB codes:
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PDB codes:
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PDB code:
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PDB code:
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Proc Natl Acad Sci U S A,
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PDB code:
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The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity.
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Immunity,
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PDB codes:
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Examination of possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins.
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Proteins,
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S.L.Lauemøller,
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S.Brunak,
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Quantitative predictions of peptide binding to MHC class I molecules using specificity matrices and anchor-stratified calibrations.
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Tissue Antigens,
57,
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PDB code:
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PDB code:
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PDB code:
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| |
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PDB code:
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K.A.Hogquist,
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PDB code:
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PDB codes:
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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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