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* Residue conservation analysis
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DOI no:
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J Mol Biol
285:645-653
(1999)
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PubMed id:
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Decamer-like conformation of a nona-peptide bound to HLA-B*3501 due to non-standard positioning of the C terminus.
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R.Menssen,
P.Orth,
A.Ziegler,
W.Saenger.
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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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Selected figure(s)
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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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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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B.Loll,
C.Rückert,
C.S.Hee,
W.Saenger,
B.Uchanska-Ziegler,
and
A.Ziegler
(2011).
Loss of recognition by cross-reactive T cells and its relation to a C-terminus-induced conformational reorientation of an HLA-B*2705-bound peptide.
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Protein Sci,
20,
278-290.
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PDB code:
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P.Kumar,
A.Vahedi-Faridi,
W.Saenger,
E.Merino,
J.A.López de Castro,
B.Uchanska-Ziegler,
and
A.Ziegler
(2009).
Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens.
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J Biol Chem,
284,
29784-29797.
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PDB codes:
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B.Sanjanwala,
M.Draghi,
P.J.Norman,
L.A.Guethlein,
and
P.Parham
(2008).
Polymorphic sites away from the Bw4 epitope that affect interaction of Bw4+ HLA-B with KIR3DL1.
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J Immunol,
181,
6293-6300.
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K.Winkler,
A.Winter,
C.Rueckert,
B.Uchanska-Ziegler,
and
U.Alexiev
(2007).
Natural MHC class I polymorphism controls the pathway of peptide dissociation from HLA-B27 complexes.
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Biophys J,
93,
2743-2755.
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A.J.Bordner,
and
R.Abagyan
(2006).
Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes.
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Proteins,
63,
512-526.
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C.Rückert,
M.T.Fiorillo,
B.Loll,
R.Moretti,
J.Biesiadka,
W.Saenger,
A.Ziegler,
R.Sorrentino,
and
B.Uchanska-Ziegler
(2006).
Conformational dimorphism of self-peptides and molecular mimicry in a disease-associated HLA-B27 subtype.
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J Biol Chem,
281,
2306-2316.
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PDB code:
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F.E.Tynan,
D.Elhassen,
A.W.Purcell,
J.M.Burrows,
N.A.Borg,
J.J.Miles,
N.A.Williamson,
K.J.Green,
J.Tellam,
L.Kjer-Nielsen,
J.McCluskey,
J.Rossjohn,
and
S.R.Burrows
(2005).
The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation.
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J Exp Med,
202,
1249-1260.
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PDB codes:
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F.E.Tynan,
N.A.Borg,
J.J.Miles,
T.Beddoe,
D.El-Hassen,
S.L.Silins,
W.J.van Zuylen,
A.W.Purcell,
L.Kjer-Nielsen,
J.McCluskey,
S.R.Burrows,
and
J.Rossjohn
(2005).
High resolution structures of highly bulged viral epitopes bound to major histocompatibility complex class I. Implications for T-cell receptor engagement and T-cell immunodominance.
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J Biol Chem,
280,
23900-23909.
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PDB codes:
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M.Hülsmeyer,
P.Chames,
R.C.Hillig,
R.L.Stanfield,
G.Held,
P.G.Coulie,
C.Alings,
G.Wille,
W.Saenger,
B.Uchanska-Ziegler,
H.R.Hoogenboom,
and
A.Ziegler
(2005).
A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA)-A1-MAGE-A1 in complex with FAB-HYB3.
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J Biol Chem,
280,
2972-2980.
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PDB code:
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A.Korostelev,
M.O.Fenley,
and
M.S.Chapman
(2004).
Impact of a Poisson-Boltzmann electrostatic restraint on protein structures refined at medium resolution.
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Acta Crystallogr D Biol Crystallogr,
60,
1786-1794.
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M.Hülsmeyer,
M.T.Fiorillo,
F.Bettosini,
R.Sorrentino,
W.Saenger,
A.Ziegler,
and
B.Uchanska-Ziegler
(2004).
Dual, HLA-B27 subtype-dependent conformation of a self-peptide.
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J Exp Med,
199,
271-281.
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PDB codes:
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R.C.Hillig,
M.Hülsmeyer,
W.Saenger,
K.Welfle,
R.Misselwitz,
H.Welfle,
C.Kozerski,
A.Volz,
B.Uchanska-Ziegler,
and
A.Ziegler
(2004).
Thermodynamic and structural analysis of peptide- and allele-dependent properties of two HLA-B27 subtypes exhibiting differential disease association.
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J Biol Chem,
279,
652-663.
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PDB code:
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Z.Yang,
L.Shipman,
M.Zhang,
B.P.Anton,
R.J.Roberts,
and
X.Cheng
(2004).
Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase.
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J Mol Biol,
340,
695-706.
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PDB code:
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W.A.Macdonald,
A.W.Purcell,
N.A.Mifsud,
L.K.Ely,
D.S.Williams,
L.Chang,
J.J.Gorman,
C.S.Clements,
L.Kjer-Nielsen,
D.M.Koelle,
S.R.Burrows,
B.D.Tait,
R.Holdsworth,
A.G.Brooks,
G.O.Lovrecz,
L.Lu,
J.Rossjohn,
and
J.McCluskey
(2003).
A naturally selected dimorphism within the HLA-B44 supertype alters class I structure, peptide repertoire, and T cell recognition.
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J Exp Med,
198,
679-691.
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PDB codes:
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F.Fabiola,
R.Bertram,
A.Korostelev,
and
M.S.Chapman
(2002).
An improved hydrogen bond potential: impact on medium resolution protein structures.
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Protein Sci,
11,
1415-1423.
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P.E.Adrian,
G.Rajaseger,
V.S.Mathura,
M.K.Sakharkar,
and
P.Kangueane
(2002).
Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data.
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| |
BMC Struct Biol,
2,
2.
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M.Probst-Kepper,
V.Stroobant,
R.Kridel,
B.Gaugler,
C.Landry,
F.Brasseur,
J.P.Cosyns,
B.Weynand,
T.Boon,
and
B.J.Van Den Eynde
(2001).
An alternative open reading frame of the human macrophage colony-stimulating factor gene is independently translated and codes for an antigenic peptide of 14 amino acids recognized by tumor-infiltrating CD8 T lymphocytes.
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J Exp Med,
193,
1189-1198.
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A.Simon,
Z.Dosztányi,
E.Rajnavölgyi,
and
I.Simon
(2000).
Function-related regulation of the stability of MHC proteins.
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| |
Biophys J,
79,
2305-2313.
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O.Schueler-Furman,
Y.Altuvia,
A.Sette,
and
H.Margalit
(2000).
Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles.
|
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Protein Sci,
9,
1838-1846.
|
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K.Maenaka,
and
E.Y.Jones
(1999).
MHC superfamily structure and the immune system.
|
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Curr Opin Struct Biol,
9,
745-753.
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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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Links
