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PDBsum entry 1a9b
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Complex (mhc class i/peptide)
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PDB id
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1a9b
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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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Decamer-Like conformation of a nona-Peptide bound to hla-B3501 Due to non-Standard positioning of the c terminus.
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Authors
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R.Menssen,
P.Orth,
A.Ziegler,
W.Saenger.
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Ref.
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J Mol Biol, 1999,
285,
645-653.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
90%.
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Abstract
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The N and C termini of peptides presented by major histocompatibility complex
(MHC) class I molecules are held within the peptide binding groove by a network
of hydrogen bonds to conserved MHC residues. However, the published structure of
the human allele HLA-B*3501 complexed with the nef octa-peptide VPLRPMTY,
revealed non-standard positioning for both peptide termini. To investigate
whether these deviations are indeed related to the length of the nef-peptide, we
have determined the structure of HLA-B*3501 presenting a nona-peptide to 2.5 A
resolution. A comparison of HLA-B*3501/peptide complexes with structures of
other HLA molecules exhibits allele-specific properties of HLA-B*3501, as well
as peptide-induced structural changes. Independent of the length of the bound
peptide, HLA-B*3501 positions the peptide C terminus significantly closer to the
alpha1-helix and nearer to the A pocket than observed for other HLA class
I/peptide complexes. This reorientation is accompanied by a shift within the
N-terminal part of the alpha2-helix towards the middle of the binding groove.
Due to the short distance between the N and C termini, the nona-peptide is
compressed and forced to zig-zag vertically within the binding groove. Its
conformation rather resembles that of a deca-peptide than of other nona-peptides
bound to class I molecules. Superposition of both HLA-B*3501/peptide complexes
additionally reveals a significant, peptide-dependent deviation between the
N-terminal parts of the alpha1-helices which might be due to different
positioning of the peptide N termini. Taken together, these data illustrate the
strong interdependence between the HLA class I molecule and the bound peptide.
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Figure 3.
Figure 3. Representation of the two equivalent positions of
Tyr99. The generally observed position (shown in light gray)
enables hydrogen-bonding to Tyr9 and usually to the P3 nitrogen,
while the alternative orientation (dark) in HLA-B*3501 allows
interaction with the side-chain of aspartate at position 5 of
the peptide (P D5).
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Figure 4.
Figure 4. Stereo-view of the peptide N terminus and the
adjacent helices of the B*3501/ebna (red) and B*3501/nef
(yellow) molecules. Hydrogen-bonding interactions, involving one
water molecule (blue), are shown for the B*3501/ebna complex.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
285,
645-653)
copyright 1999.
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