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* Residue conservation analysis
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PDB id:
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Histocompatibility complex
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Title:
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Antagonist HIV-1 gag peptides induce structural changes in hla b8-HIV- 1 gag peptide (ggkkrykl-5r mutation)
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Structure:
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B 0801. Chain: a. Fragment: extracellular. Synonym: b8. Engineered: yes. Beta-2 microglobulin. Chain: b. Fragment: extracellular. Synonym: b2m.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Cell_line: xa90. Gene: gag. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21(de3)plyss. Expression_system_cell_line: xa90.
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Biol. unit:
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Trimer (from
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Resolution:
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Authors:
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S.W.Reid,S.Mcadam,K.J.Smith,P.Klenerman,C.A.O'Callaghan,K.Harlos, B.K.Jakobsen,A.J.Mcmichael,J.Bell,D.I.Stuart,E.Y.Jones
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Key ref:
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S.W.Reid
et al.
(1996).
Antagonist HIV-1 Gag peptides induce structural changes in HLA B8.
J Exp Med,
184,
2279-2286.
PubMed id:
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Date:
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24-Mar-97
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Release date:
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16-Jun-97
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PROCHECK
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Headers
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References
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J Exp Med
184:2279-2286
(1996)
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PubMed id:
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Antagonist HIV-1 Gag peptides induce structural changes in HLA B8.
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S.W.Reid,
S.McAdam,
K.J.Smith,
P.Klenerman,
C.A.O'Callaghan,
K.Harlos,
B.K.Jakobsen,
A.J.McMichael,
J.I.Bell,
D.I.Stuart,
E.Y.Jones.
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ABSTRACT
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In the cellular immune response, recognition by CTL-TCRs of viral antigens
presented as peptides by HLA class I molecules, triggers destruction of the
virally infected cell (Townsend, A.R.M., J. Rothbard, F.M. Gotch, G. Bahadur, D.
Wraith, and A.J. McMichael. 1986. Cell. 44:959-968). Altered peptide ligands
(APLs) which antagonise CTL recognition of infected cells have been reported
(Jameson, S.C., F.R. Carbone, and M.J. Bevan. 1993. J. Exp. Med. 177:1541-1550).
In one example, lysis of antigen presenting cells by CTLs in response to
recognition of an HLA B8-restricted HIV-1 P17 (aa 24-31) epitope can be
inhibited by naturally occurring variants of this peptide, which act as TCR
antagonists (Klenerman, P., S. Rowland Jones, S. McAdam, J. Edwards, S. Daenke,
D. Lalloo, B. Koppe, W. Rosenberg, D. Boyd, A. Edwards, P. Giangrande, R.E.
Phillips, and A. McMichael. 1994. Nature (Lond.). 369:403-407). We have
characterised two CTL clones and a CTL line whose interactions with these
variants of P17 (aa 24-31) exhibit a variety of responses. We have examined the
high resolution crystal structures of four of these APLs in complex with HLA B8
to determine alterations in the shape, chemistry, and local flexibility of the
TCR binding surface. The variant peptides cause changes in the recognition
surface by three mechanisms: changes contributed directly by the peptide,
effects transmitted to the exposed peptide surface, and induced effects on the
exposed framework of the peptide binding groove. While the first two mechanisms
frequently lead to antagonism, the third has more profound effects on TCR
recognition.
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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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K.M.Miles,
J.J.Miles,
F.Madura,
A.K.Sewell,
and
D.K.Cole
(2011).
Real time detection of peptide-MHC dissociation reveals that improvement of primary MHC-binding residues can have a minimal, or no, effect on stability.
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Mol Immunol,
48,
728-732.
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A.Theodossis,
C.Guillonneau,
A.Welland,
L.K.Ely,
C.S.Clements,
N.A.Williamson,
A.I.Webb,
J.A.Wilce,
R.J.Mulder,
M.A.Dunstone,
P.C.Doherty,
J.McCluskey,
A.W.Purcell,
S.J.Turner,
and
J.Rossjohn
(2010).
Constraints within major histocompatibility complex class I restricted peptides: presentation and consequences for T-cell recognition.
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Proc Natl Acad Sci U S A,
107,
5534-5539.
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PDB codes:
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A.Van Hateren,
E.James,
A.Bailey,
A.Phillips,
N.Dalchau,
and
T.Elliott
(2010).
The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding.
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Tissue Antigens,
76,
259-275.
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B.Guinn,
G.Casey,
M.G.Möller,
N.Kasahara,
G.C.O'Sullivan,
K.W.Peng,
and
M.Tangney
(2010).
International Society for Cell and Gene Therapy of Cancer 2009 Annual Meeting held in Cork, Ireland.
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| |
Hum Gene Ther,
21,
9.
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Y.Sun,
J.Liu,
M.Yang,
F.Gao,
J.Zhou,
Y.Kitamura,
B.Gao,
P.Tien,
Y.Shu,
A.Iwamoto,
Z.Chen,
and
G.F.Gao
(2010).
Identification and structural definition of H5-specific CTL epitopes restricted by HLA-A*0201 derived from the H5N1 subtype of influenza A viruses.
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J Gen Virol,
91,
919-930.
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PDB codes:
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D.I.Godfrey,
J.Rossjohn,
and
J.McCluskey
(2008).
The fidelity, occasional promiscuity, and versatility of T cell receptor recognition.
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| |
Immunity,
28,
304-314.
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V.Sanchez-Merino,
M.A.Farrow,
F.Brewster,
M.Somasundaran,
and
K.Luzuriaga
(2008).
Identification and characterization of HIV-1 CD8+ T cell escape variants with impaired fitness.
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J Infect Dis,
197,
300-308.
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C.Bade-Doeding,
D.S.DeLuca,
A.Seltsam,
R.Blasczyk,
and
B.Eiz-Vesper
(2007).
Amino acid 95 causes strong alteration of peptide position Pomega in HLA-B*41 variants.
|
| |
Immunogenetics,
59,
253-259.
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|
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C.McCarthy,
D.Shepherd,
S.Fleire,
V.S.Stronge,
M.Koch,
P.A.Illarionov,
G.Bossi,
M.Salio,
G.Denkberg,
F.Reddington,
A.Tarlton,
B.G.Reddy,
R.R.Schmidt,
Y.Reiter,
G.M.Griffiths,
P.A.van der Merwe,
G.S.Besra,
E.Y.Jones,
F.D.Batista,
and
V.Cerundolo
(2007).
The length of lipids bound to human CD1d molecules modulates the affinity of NKT cell TCR and the threshold of NKT cell activation.
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| |
J Exp Med,
204,
1131-1144.
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M.Koch,
S.Camp,
T.Collen,
D.Avila,
J.Salomonsen,
H.J.Wallny,
A.van Hateren,
L.Hunt,
J.P.Jacob,
F.Johnston,
D.A.Marston,
I.Shaw,
P.R.Dunbar,
V.Cerundolo,
E.Y.Jones,
and
J.Kaufman
(2007).
Structures of an MHC class I molecule from B21 chickens illustrate promiscuous peptide binding.
|
| |
Immunity,
27,
885-899.
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PDB codes:
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P.Zimbwa,
A.Milicic,
J.Frater,
T.J.Scriba,
A.Willis,
P.J.Goulder,
T.Pillay,
H.Gunthard,
J.N.Weber,
H.T.Zhang,
and
R.E.Phillips
(2007).
Precise identification of a human immunodeficiency virus type 1 antigen processing mutant.
|
| |
J Virol,
81,
2031-2038.
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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.
|
| |
Proteins,
63,
512-526.
|
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|
|
|
|
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D.K.Cole,
P.J.Rizkallah,
F.Gao,
N.I.Watson,
J.M.Boulter,
J.I.Bell,
M.Sami,
G.F.Gao,
and
B.K.Jakobsen
(2006).
Crystal structure of HLA-A*2402 complexed with a telomerase peptide.
|
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Eur J Immunol,
36,
170-179.
|
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PDB code:
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M.López,
V.Soriano,
S.Lozano,
P.Martinez,
J.Sempere,
J.González-Lahoz,
and
J.Benito
(2006).
Impact of Gag sequence variability on level, phenotype, and function of anti-HIV Gag-specific CD8(+) cytotoxic T lymphocytes in untreated chronically HIV-infected patients.
|
| |
AIDS Res Hum Retroviruses,
22,
884-892.
|
|
|
|
|
|
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P.J.Norris,
J.D.Stone,
N.Anikeeva,
J.W.Heitman,
I.C.Wilson,
D.F.Hirschkorn,
M.J.Clark,
H.F.Moffett,
T.O.Cameron,
Y.Sykulev,
L.J.Stern,
and
B.D.Walker
(2006).
Antagonism of HIV-specific CD4+ T cells by C-terminal truncation of a minimum epitope.
|
| |
Mol Immunol,
43,
1349-1357.
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|
|
A.Milicic,
C.T.Edwards,
S.Hué,
J.Fox,
H.Brown,
T.Pillay,
J.W.Drijfhout,
J.N.Weber,
E.C.Holmes,
S.J.Fidler,
H.T.Zhang,
and
R.E.Phillips
(2005).
Sexual transmission of single human immunodeficiency virus type 1 virions encoding highly polymorphic multisite cytotoxic T-lymphocyte escape variants.
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| |
J Virol,
79,
13953-13962.
|
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|
|
|
|
|
B.Barugahare,
C.Baker,
O.K'Aluoch,
R.Donovan,
M.Elrefaei,
M.Eggena,
N.Jones,
S.Mutalya,
C.Kityo,
P.Mugyenyi,
and
H.Cao
(2005).
Human immunodeficiency virus-specific responses in adult Ugandans: patterns of cross-clade recognition.
|
| |
J Virol,
79,
4132-4139.
|
|
|
|
|
|
|
J.L.Chen,
G.Stewart-Jones,
G.Bossi,
N.M.Lissin,
L.Wooldridge,
E.M.Choi,
G.Held,
P.R.Dunbar,
R.M.Esnouf,
M.Sami,
J.M.Boulter,
P.Rizkallah,
C.Renner,
A.Sewell,
P.A.van der Merwe,
B.K.Jakobsen,
G.Griffiths,
E.Y.Jones,
and
V.Cerundolo
(2005).
Structural and kinetic basis for heightened immunogenicity of T cell vaccines.
|
| |
J Exp Med,
201,
1243-1255.
|
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PDB codes:
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O.Y.Borbulevych,
T.K.Baxter,
Z.Yu,
N.P.Restifo,
and
B.M.Baker
(2005).
Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design.
|
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J Immunol,
174,
4812-4820.
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PDB codes:
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S.Oerke,
H.Höhn,
I.Zehbe,
H.Pilch,
K.H.Schicketanz,
W.E.Hitzler,
C.Neukirch,
K.Freitag,
and
M.J.Maeurer
(2005).
Naturally processed and HLA-B8-presented HPV16 E7 epitope recognized by T cells from patients with cervical cancer.
|
| |
Int J Cancer,
114,
766-778.
|
|
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|
D.A.Price,
S.M.West,
M.R.Betts,
L.E.Ruff,
J.M.Brenchley,
D.R.Ambrozak,
Y.Edghill-Smith,
M.J.Kuroda,
D.Bogdan,
K.Kunstman,
N.L.Letvin,
G.Franchini,
S.M.Wolinsky,
R.A.Koup,
and
D.C.Douek
(2004).
T cell receptor recognition motifs govern immune escape patterns in acute SIV infection.
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| |
Immunity,
21,
793-803.
|
|
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|
J.K.Lee,
G.Stewart-Jones,
T.Dong,
K.Harlos,
K.Di Gleria,
L.Dorrell,
D.C.Douek,
P.A.van der Merwe,
E.Y.Jones,
and
A.J.McMichael
(2004).
T cell cross-reactivity and conformational changes during TCR engagement.
|
| |
J Exp Med,
200,
1455-1466.
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PDB codes:
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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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T.Dong,
G.Stewart-Jones,
N.Chen,
P.Easterbrook,
X.Xu,
L.Papagno,
V.Appay,
M.Weekes,
C.Conlon,
C.Spina,
S.Little,
G.Screaton,
A.van der Merwe,
D.D.Richman,
A.J.McMichael,
E.Y.Jones,
and
S.L.Rowland-Jones
(2004).
HIV-specific cytotoxic T cells from long-term survivors select a unique T cell receptor.
|
| |
J Exp Med,
200,
1547-1557.
|
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S.Vukmanović,
T.A.Neubert,
and
F.R.Santori
(2003).
Could TCR antagonism explain associations between MHC genes and disease?
|
| |
Trends Mol Med,
9,
139-146.
|
|
|
|
|
|
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A.Achour,
J.Michaëlsson,
R.A.Harris,
J.Odeberg,
P.Grufman,
J.K.Sandberg,
V.Levitsky,
K.Kärre,
T.Sandalova,
and
G.Schneider
(2002).
A structural basis for LCMV immune evasion: subversion of H-2D(b) and H-2K(b) presentation of gp33 revealed by comparative crystal structure.Analyses.
|
| |
Immunity,
17,
757-768.
|
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PDB codes:
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A.McMichael,
and
T.Hanke
(2002).
The quest for an AIDS vaccine: is the CD8+ T-cell approach feasible?
|
| |
Nat Rev Immunol,
2,
283-291.
|
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|
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J.Hennecke,
and
D.C.Wiley
(2002).
Structure of a complex of the human alpha/beta T cell receptor (TCR) HA1.7, influenza hemagglutinin peptide, and major histocompatibility complex class II molecule, HLA-DR4 (DRA*0101 and DRB1*0401): insight into TCR cross-restriction and alloreactivity.
|
| |
J Exp Med,
195,
571-581.
|
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PDB code:
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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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F.Lechner,
A.L.Cuero,
M.Kantzanou,
and
P.Klenerman
(2001).
Studies of human antiviral CD8+ lymphocytes using class I peptide tetramers.
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| |
Rev Med Virol,
11,
11-22.
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M.Regner
(2001).
Cross-reactivity in T-cell antigen recognition.
|
| |
Immunol Cell Biol,
79,
91.
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|
O.Schueler-Furman,
Y.Altuvia,
and
H.Margalit
(2001).
Examination of possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins.
|
| |
Proteins,
45,
47-54.
|
|
|
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|
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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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|
F.Lechner,
J.Sullivan,
H.Spiegel,
D.F.Nixon,
B.Ferrari,
A.Davis,
B.Borkowsky,
H.Pollack,
E.Barnes,
G.Dusheiko,
and
P.Klenerman
(2000).
Why do cytotoxic T lymphocytes fail to eliminate hepatitis C virus? Lessons from studies using major histocompatibility complex class I peptide tetramers.
|
| |
Philos Trans R Soc Lond B Biol Sci,
355,
1085-1092.
|
|
|
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|
|
J.T.Voeten,
T.M.Bestebroer,
N.J.Nieuwkoop,
R.A.Fouchier,
A.D.Osterhaus,
and
G.F.Rimmelzwaan
(2000).
Antigenic drift in the influenza A virus (H3N2) nucleoprotein and escape from recognition by cytotoxic T lymphocytes.
|
| |
J Virol,
74,
6800-6807.
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M.C.Barnardo,
A.W.Harmer,
O.J.Shaw,
G.S.Ogg,
M.Bunce,
R.W.Vaughan,
P.J.Morris,
and
K.I.Welsh
(2000).
Detection of HLA-specific IGG antibodies using single recombinant HLA alleles: the MonoLISA assay.
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Transplantation,
70,
531-536.
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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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J.A.Speir,
U.M.Abdel-Motal,
M.Jondal,
and
I.A.Wilson
(1999).
Crystal structure of an MHC class I presented glycopeptide that generates carbohydrate-specific CTL.
|
| |
Immunity,
10,
51-61.
|
|
|
PDB code:
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|
|
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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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A.J.McMichael,
and
C.A.O'Callaghan
(1998).
A new look at T cells.
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J Exp Med,
187,
1367-1371.
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E.J.Collins,
and
J.A.Frelinger
(1998).
Altered peptide ligand design: altering immune responses to class I MHC/peptide complexes.
|
| |
Immunol Rev,
163,
151-160.
|
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|
E.Y.Jones,
J.Tormo,
S.W.Reid,
and
D.I.Stuart
(1998).
Recognition surfaces of MHC class I.
|
| |
Immunol Rev,
163,
121-128.
|
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|
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|
P.Borrow,
and
G.M.Shaw
(1998).
Cytotoxic T-lymphocyte escape viral variants: how important are they in viral evasion of immune clearance in vivo?
|
| |
Immunol Rev,
164,
37-51.
|
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|
Y.Ghendler,
M.K.Teng,
J.H.Liu,
T.Witte,
J.Liu,
K.S.Kim,
P.Kern,
H.C.Chang,
J.H.Wang,
and
E.L.Reinherz
(1998).
Differential thymic selection outcomes stimulated by focal structural alteration in peptide/major histocompatibility complex ligands.
|
| |
Proc Natl Acad Sci U S A,
95,
10061-10066.
|
|
|
PDB code:
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|
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|
Y.H.Ding,
K.J.Smith,
D.N.Garboczi,
U.Utz,
W.E.Biddison,
and
D.C.Wiley
(1998).
Two human T cell receptors bind in a similar diagonal mode to the HLA-A2/Tax peptide complex using different TCR amino acids.
|
| |
Immunity,
8,
403-411.
|
|
|
PDB code:
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|
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|
|
|
A.K.Sewell,
G.C.Harcourt,
P.J.Goulder,
D.A.Price,
and
R.E.Phillips
(1997).
Antagonism of cytotoxic T lymphocyte-mediated lysis by natural HIV-1 altered peptide ligands requires simultaneous presentation of agonist and antagonist peptides.
|
| |
Eur J Immunol,
27,
2323-2329.
|
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|
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G.Dadaglio,
C.A.Nelson,
M.B.Deck,
S.J.Petzold,
and
E.R.Unanue
(1997).
Characterization and quantitation of peptide-MHC complexes produced from hen egg lysozyme using a monoclonal antibody.
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Immunity,
6,
727-738.
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K.D.Smith,
Z.B.Kurago,
and
C.T.Lutz
(1997).
Conformational changes in MHC class I molecules. Antibody, T-cell receptor, and NK cell recognition in an HLA-B7 model system.
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| |
Immunol Res,
16,
243-259.
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P.Goulder,
D.Price,
M.Nowak,
S.Rowland-Jones,
R.Phillips,
and
A.McMichael
(1997).
Co-evolution of human immunodeficiency virus and cytotoxic T-lymphocyte responses.
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Immunol Rev,
159,
17-29.
|
|
|
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P.J.Goulder,
S.W.Reid,
D.A.Price,
C.A.O'Callaghan,
A.J.McMichael,
R.E.Phillips,
and
E.Y.Jones
(1997).
Combined structural and immunological refinement of HIV-1 HLA-B8-restricted cytotoxic T lymphocyte epitopes.
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Eur J Immunol,
27,
1515-1521.
|
|
|
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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
codes are
shown on the right.
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