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* Residue conservation analysis
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Nature
342:692-696
(1989)
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PubMed id:
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Specificity pockets for the side chains of peptide antigens in HLA-Aw68.
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T.P.Garrett,
M.A.Saper,
P.J.Bjorkman,
J.L.Strominger,
D.C.Wiley.
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ABSTRACT
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We have determined the structure of a second human histocompatibility
glycoprotein, HLA-Aw68, by X-ray crystallography and refined it to a resolution
of 2.6 A. Overall, the structure is extremely similar to that of HLA-A2 (refs 1,
2; and M.A.S. et al., manuscript in preparation), although the 11 amino-acid
substitutions at polymorphic residues in the antigen-binding cleft alter the
detailed shape and electrostatic charge of that site. A prominent negatively
charged pocket within the cleft extends underneath the alpha-helix of the alpha
1-domain, providing a potential subsite for recognizing a positively charged
side chain or peptide N terminus. Uninterpreted electron density, presumably
representing an unknown 'antigen(s)', which seems to be different from that seen
in the HLA-A2 structure, occupies the cleft and extends into the negatively
charged pocket in HLA-Aw68. The structures of HLA-Aw68 and HLA-A2 demonstrate
how polymorphism creates and alters subsites (pockets) positioned to bind
peptide side chains, thereby suggesting the structural basis for allelic
specificity in foreign antigen binding.
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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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L.Kjer-Nielsen,
O.Patel,
A.J.Corbett,
J.Le Nours,
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N.A.Williamson,
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N.L.Dudek,
M.J.McConville,
R.A.O'Hair,
G.N.Khairallah,
D.I.Godfrey,
D.P.Fairlie,
J.Rossjohn,
and
J.McCluskey
(2012).
MR1 presents microbial vitamin B metabolites to MAIT cells.
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Nature,
491,
717-723.
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PDB code:
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J.Hinrichs,
D.Föll,
C.Bade-Döding,
T.Huyton,
R.Blasczyk,
and
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The nature of peptides presented by an HLA class I low expression allele.
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Haematologica,
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HLA-A disparities illustrate challenges for ranking the impact of HLA mismatches on bone marrow transplant outcomes in the United States.
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In vivo detection of residues required for ligand-selective activation of the S-locus receptor in Arabidopsis.
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Curr Biol,
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Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets.
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Amino acid 95 causes strong alteration of peptide position Pomega in HLA-B*41 variants.
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Immunogenetics,
59,
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Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4.
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Functional and biophysical characterization of an HLA-A*6801-restricted HIV-specific T cell receptor.
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Eur J Immunol,
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J.T.Loffredo,
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C.E.Glidden,
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Mamu-B*08-positive macaques control simian immunodeficiency virus replication.
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J Virol,
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J.T.Loffredo,
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and
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CD8 T Cells from SIV Elite Controller Macaques Recognize Mamu-B*08-Bound Epitopes and Select for Widespread Viral Variation.
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PLoS ONE,
2,
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S.Y.Choo
(2007).
The HLA system: genetics, immunology, clinical testing, and clinical implications.
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Yonsei Med J,
48,
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C.Thilo,
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J.W.Yewdell,
H.G.Ljunggren,
and
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(2006).
Dissection of the interaction of the human cytomegalovirus-derived US2 protein with major histocompatibility complex class I molecules: prominent role of a single arginine residue in human leukocyte antigen-A2.
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J Biol Chem,
281,
8950-8957.
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J.L.Strominger,
and
J.L.Strominger
(2006).
The tortuous journey of a biochemist to immunoland and what he found there.
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Annu Rev Immunol,
24,
1.
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K.Natarajan,
A.Hicks,
J.Mans,
H.Robinson,
R.Guan,
R.A.Mariuzza,
and
D.H.Margulies
(2006).
Crystal structure of the murine cytomegalovirus MHC-I homolog m144.
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J Mol Biol,
358,
157-171.
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PDB code:
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N.Mehra,
and
G.Kaur
(2006).
HLA genetics and disease with particular reference to Type 1 diabetes and HIV infection in Asian Indians.
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Expert Rev Clin Immunol,
2,
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P.J.Bjorkman
(2006).
Finding the groove.
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Nat Immunol,
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T.Blicher,
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S.Buus,
and
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(2006).
Structure of HLA-A*1101 in complex with a hepatitis B peptide homologue.
|
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
62,
1179-1184.
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PDB code:
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V.Mitaksov,
and
D.H.Fremont
(2006).
Structural definition of the H-2Kd peptide-binding motif.
|
| |
J Biol Chem,
281,
10618-10625.
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PDB code:
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E.Merino,
V.Montserrat,
A.Paradela,
and
J.A.López de Castro
(2005).
Two HLA-B14 subtypes (B*1402 and B*1403) differentially associated with ankylosing spondylitis differ substantially in peptide specificity but have limited peptide and T-cell epitope sharing with HLA-B27.
|
| |
J Biol Chem,
280,
35868-35880.
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N.Frahm,
S.Adams,
P.Kiepiela,
C.H.Linde,
H.S.Hewitt,
M.Lichterfeld,
K.Sango,
N.V.Brown,
E.Pae,
A.G.Wurcel,
M.Altfeld,
M.E.Feeney,
T.M.Allen,
T.Roach,
M.A.St John,
E.S.Daar,
E.Rosenberg,
B.Korber,
F.Marincola,
B.D.Walker,
P.J.Goulder,
and
C.Brander
(2005).
HLA-B63 presents HLA-B57/B58-restricted cytotoxic T-lymphocyte epitopes and is associated with low human immunodeficiency virus load.
|
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J Virol,
79,
10218-10225.
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T.Blicher,
J.S.Kastrup,
S.Buus,
and
M.Gajhede
(2005).
High-resolution structure of HLA-A*1101 in complex with SARS nucleocapsid peptide.
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Acta Crystallogr D Biol Crystallogr,
61,
1031-1040.
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PDB code:
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V.Apostolopoulos,
and
E.Lazoura
(2004).
Noncanonical peptides in complex with MHC class I.
|
| |
Expert Rev Vaccines,
3,
151-162.
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C.J.Cohen,
G.Denkberg,
A.Lev,
M.Epel,
and
Y.Reiter
(2003).
Recombinant antibodies with MHC-restricted, peptide-specific, T-cell receptor-like specificity: new tools to study antigen presentation and TCR-peptide-MHC interactions.
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| |
J Mol Recognit,
16,
324-332.
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D.G.Lim,
J.M.Slavik,
K.Bourcier,
K.J.Smith,
and
D.A.Hafler
(2003).
Allelic variation of MHC structure alters peptide ligands to induce atypical partial agonistic CD8+ T cell function.
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| |
J Exp Med,
198,
99.
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H.Nojima,
M.Takeda-Shitaka,
Y.Kurihara,
K.Kamiya,
and
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(2003).
Dynamic flexibility of a peptide-binding groove of human HLA-DR1 class II MHC molecules: normal mode analysis of the antigen peptide-class II MHC complex.
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| |
Chem Pharm Bull (Tokyo),
51,
923-928.
|
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M.K.Dankers,
D.L.Roelen,
E.M.Van Der Meer-Prins,
P.De Lange,
N.Korfage,
J.M.Smits,
G.G.Persijn,
K.I.Welsh,
I.I.Doxiadis,
and
F.H.Claas
(2003).
Differential immunogenicity of HLA mismatches: HLA-A2 versus HLA-A28.
|
| |
Transplantation,
75,
418-420.
|
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|
|
|
V.Apostolopoulos,
E.Yuriev,
P.A.Ramsland,
J.Halton,
C.Osinski,
W.Li,
M.Plebanski,
H.Paulsen,
and
I.F.McKenzie
(2003).
A glycopeptide in complex with MHC class I uses the GalNAc residue as an anchor.
|
| |
Proc Natl Acad Sci U S A,
100,
15029-15034.
|
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|
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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.
|
| |
J Exp Med,
198,
679-691.
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PDB codes:
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H.A.Elsner,
and
R.Blasczyk
(2002).
Sequence similarity matching: proposal of a structure-based rating system for bone marrow transplantation.
|
| |
Eur J Immunogenet,
29,
229-236.
|
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|
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|
|
H.Nojima,
M.Takeda-Shitaka,
Y.Kurihara,
M.Adachi,
S.Yoneda,
K.Kamiya,
and
H.Umeyama
(2002).
Dynamic characteristics of a peptide-binding groove of human HLA-A2 class I MHC molecules: normal mode analysis of the antigen peptide-class I MHC complex.
|
| |
Chem Pharm Bull (Tokyo),
50,
1209-1214.
|
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|
M.J.Maeurer,
A.Necker,
R.D.Salter,
C.Castelli,
H.Höhn,
J.Karbach,
K.Freitag,
C.Neukirch,
A.Knuth,
and
E.Jäger
(2002).
Improved detection of melanoma antigen-specific T cells expressing low or high levels of CD8 by HLA-A2 tetramers presenting a Melan-A/Mart-1 peptide analogue.
|
| |
Int J Cancer,
97,
64-71.
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M.Przemeck,
H.A.Elsner,
S.Sel,
L.T.Pastucha,
and
R.Blasczyk
(2002).
HLA-B*4431: a new HLA-B variant with a complex ancestral history involving HLA-B*44, B*40 and B*07 alleles.
|
| |
Tissue Antigens,
60,
91-94.
|
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X.Liu,
S.Dai,
F.Crawford,
R.Fruge,
P.Marrack,
and
J.Kappler
(2002).
Alternate interactions define the binding of peptides to the MHC molecule IA(b).
|
| |
Proc Natl Acad Sci U S A,
99,
8820-8825.
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PDB code:
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J.Yague,
A.Marina,
J.Vazquez,
and
J.A.Lopez De Castro
(2001).
Major histocompatibility complex class I molecules bind natural peptide ligands lacking the amino-terminal binding residue in vivo.
|
| |
J Biol Chem,
276,
43699-43707.
|
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S.Hanabuchi,
T.Ohashi,
Y.Koya,
H.Kato,
A.Hasegawa,
F.Takemura,
T.Masuda,
and
M.Kannagi
(2001).
Regression of human T-cell leukemia virus type I (HTLV-I)-associated lymphomas in a rat model: peptide-induced T-cell immunity.
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J Natl Cancer Inst,
93,
1775-1783.
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S.L.Lauemøller,
A.Holm,
J.Hilden,
S.Brunak,
M.Holst Nissen,
A.Stryhn,
L.Østergaard Pedersen,
and
S.Buus
(2001).
Quantitative predictions of peptide binding to MHC class I molecules using specificity matrices and anchor-stratified calibrations.
|
| |
Tissue Antigens,
57,
405-414.
|
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|
|
|
H.A.Elsner,
A.Wölpl,
S.F.Goldmann,
and
R.Blasczyk
(2000).
Identification of the novel allele HLA-B*1546 which belongs to the serological B72 type: implications for bone marrow transplantation.
|
| |
Tissue Antigens,
55,
83-85.
|
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|
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|
|
H.A.Elsner,
L.T.Pastucha,
V.Rebmann,
H.Grosse-Wilde,
and
R.Blasczyk
(2000).
Identification of the novel allele HLA-A*6813 in two members of a family of Syrian origin: implications for bone marrow transplantation.
|
| |
Tissue Antigens,
55,
262-265.
|
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|
|
|
|
H.A.Elsner,
and
R.Blasczyk
(2000).
Identification of the novel allele HLA-B*0809 in a Caucasian individual: estimation of allogeneic potential between B*08 variants.
|
| |
Tissue Antigens,
55,
74-77.
|
|
|
|
|
|
|
H.A.Elsner,
and
R.Blasczyk
(2000).
Identification of the novel allele HLA-B*1545: assessment of alloreactivity in case of mismatch with other B*15 alleles.
|
| |
Tissue Antigens,
55,
80-82.
|
|
|
|
|
|
|
H.A.Elsner,
and
R.Blasczyk
(2000).
Increased diversity within the HLA-B*07 group: identification of the two novel alleles B*0709 and B*0710.
|
| |
Tissue Antigens,
56,
371-375.
|
|
|
|
|
|
|
J.Yagüe,
I.Alvarez,
D.Rognan,
M.Ramos,
J.Vázquez,
and
J.A.de Castro
(2000).
An N-acetylated natural ligand of human histocompatibility leukocyte antigen (HLA)-B39. Classical major histocompatibility complex class I proteins bind peptides with a blocked NH(2) terminus in vivo.
|
| |
J Exp Med,
191,
2083-2092.
|
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J.Yagüe,
J.Vázquez,
and
J.A.López de Castro
(2000).
A post-translational modification of nuclear proteins, N(G),N(G)-dimethyl-Arg, found in a natural HLA class I peptide ligand.
|
| |
Protein Sci,
9,
2210-2217.
|
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|
S.I.Khakoo,
R.Ling,
I.Scott,
A.I.Dodi,
T.J.Harrison,
G.M.Dusheiko,
and
J.A.Madrigal
(2000).
Cytotoxic T lymphocyte responses and CTL epitope escape mutation in HBsAg, anti-HBe positive individuals.
|
| |
Gut,
47,
137-143.
|
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|
F.Micheletti,
M.Bazzaro,
A.Canella,
M.Marastoni,
S.Traniello,
and
R.Gavioli
(1999).
The lifespan of major histocompatibility complex class I/peptide complexes determines the efficiency of cytotoxic T-lymphocyte responses.
|
| |
Immunology,
96,
411-415.
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K.Maenaka,
and
E.Y.Jones
(1999).
MHC superfamily structure and the immune system.
|
| |
Curr Opin Struct Biol,
9,
745-753.
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P.E.Jensen,
D.A.Weber,
W.P.Thayer,
L.E.Westerman,
and
C.T.Dao
(1999).
Peptide exchange in MHC molecules.
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| |
Immunol Rev,
172,
229-238.
|
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|
P.E.Jensen
(1999).
Mechanisms of antigen presentation.
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| |
Clin Chem Lab Med,
37,
179-186.
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P.E.Jensen,
D.A.Weber,
W.P.Thayer,
X.Chen,
and
C.T.Dao
(1999).
HLA-DM and the MHC class II antigen presentation pathway.
|
| |
Immunol Res,
20,
195-205.
|
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|
|
|
Q.R.Fan,
and
D.C.Wiley
(1999).
Structure of human histocompatibility leukocyte antigen (HLA)-Cw4, a ligand for the KIR2D natural killer cell inhibitory receptor.
|
| |
J Exp Med,
190,
113-123.
|
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PDB code:
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R.N.Germain,
and
I.Stefanová
(1999).
The dynamics of T cell receptor signaling: complex orchestration and the key roles of tempo and cooperation.
|
| |
Annu Rev Immunol,
17,
467-522.
|
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S.Buus
(1999).
Description and prediction of peptide-MHC binding: the 'human MHC project'.
|
| |
Curr Opin Immunol,
11,
209-213.
|
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|
S.Krebs,
D.Rognan,
and
J.A.López de Castro
(1999).
Long-range effects in protein--ligand interactions mediate peptide specificity in the human major histocompatibilty antigen HLA-B27 (B*2701).
|
| |
Protein Sci,
8,
1393-1399.
|
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T.U.Vogel,
D.T.Evans,
J.A.Urvater,
D.H.O'Connor,
A.L.Hughes,
and
D.I.Watkins
(1999).
Major histocompatibility complex class I genes in primates: co-evolution with pathogens.
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Immunol Rev,
167,
327-337.
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A.Gallimore,
T.Dumrese,
H.Hengartner,
R.M.Zinkernagel,
and
H.G.Rammensee
(1998).
Protective immunity does not correlate with the hierarchy of virus-specific cytotoxic T cell responses to naturally processed peptides.
|
| |
J Exp Med,
187,
1647-1657.
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Immunity,
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