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PDBsum entry 1a1n
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Complex (antigen/peptide)
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PDB id
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1a1n
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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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An altered position of the alpha 2 helix of mhc class i is revealed by the crystal structure of hla-B3501.
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Authors
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K.J.Smith,
S.W.Reid,
D.I.Stuart,
A.J.Mcmichael,
E.Y.Jones,
J.I.Bell.
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Ref.
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Immunity, 1996,
4,
203-213.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the human major histocompatibility complex class I B
allele HLA B*3501 complexed with the 8-mer peptide epitope HIV1 Nef 75-82
(VPLRPMTY) has been determined at 2.0 angstrom resolution. Comparison with the
crystal structure of the closely related allele HLA B*5301 reveals the
structural basis for the tyrosine specificity of the B*3501 F pocket. The
structure also reveals a novel conformation of the 8-mer peptide within the
binding groove. The positions of the peptide N and C termini are nonstandard,
but the classic pattern of hydrogen bonding to nonpolymorphic MHC class I
residues is maintained, at the N terminus by addition of a water molecule, and
at the C terminus by a substantial shift in the alpha 2 helix.
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Figure 2.
Figure 2. The Structure of the HIV1 Nef Peptide
(VPLRPMTY)The views illustrate the peptide viewed through the
α2 helix.(A) A 2.0 Å F[o]−F[c] φ[calc] electron
density map for which the Nef peptide has been omitted from the
phasing model. The electron density is contoured at 2.5 σ and
displayed in FRODO ([22]) with the current model for the
peptide.(B) A main chain superposition (SHP[39]) of the Nef
peptide (light blue) with the peptide main chains from the
following structures: HLA-B53/ls6 (red), HLA-B53/HIV2 (purple),
H-2K^b/VSV8 (dark blue), HLA-A2/flu (dark green), H-2K^b/SEV9
(yellow), H-2D^b/Flu-np (light green).(C) A superposition of the
Nef peptide (green) with the ls6 peptide KPIVQYDNF (red) from
the B53/ls6 structure.
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Figure 4.
Figure 4. The F Pockets of B3501 and B53Both panels are
viewed through the α2 helix and, as in Figure 3, the MHC main
chain is represented in green, key side chains are shown in
white, dashed lines indicate hydrogen bonds, and light blue
spheres mark the positions of tightly bound water molecules.(A)
The B3501 F pocket. The polymorphic residue (Gly) at position 83
is not visible from this angle but is solvent exposed and
located on a turn of the α1 helix adjacent to residue 82.(B)
The B53 F pocket.
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The above figures are
reprinted
by permission from Cell Press:
Immunity
(1996,
4,
203-213)
copyright 1996.
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