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* Residue conservation analysis
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PDB id:
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Immune system
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Title:
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Crystal structure of rat minor histocompatibility antigen complex rt1- aa/mtf-e.
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Structure:
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Class i major histocompatibility antigen rt1-aa. Chain: a, d. Fragment: extracellular domains. Engineered: yes. Beta-2-microglobulin. Chain: b, e. Engineered: yes. Peptide mtf-e (13n3e). Chain: c, f.
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Source:
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Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this sequence occurs naturally in rats
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Biol. unit:
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Trimer (from
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Resolution:
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2.55Å
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R-factor:
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0.222
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R-free:
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0.282
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Authors:
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J.A.Speir,J.Stevens,E.Joly,G.W.Butcher,I.A.Wilson
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Key ref:
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J.A.Speir
et al.
(2001).
Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa.
Immunity,
14,
81-92.
PubMed id:
DOI:
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Date:
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26-Jan-00
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Release date:
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28-Feb-01
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PROCHECK
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Headers
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References
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P16391
(HA12_RAT) -
RT1 class I histocompatibility antigen, AA alpha chain from Rattus norvegicus
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Seq:
Struc:
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371 a.a.
275 a.a.
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DOI no:
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Immunity
14:81-92
(2001)
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PubMed id:
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Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa.
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J.A.Speir,
J.Stevens,
E.Joly,
G.W.Butcher,
I.A.Wilson.
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ABSTRACT
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The rat MHC class Ia molecule RT1-Aa has the unusual capacity to bind long
peptides ending in arginine, such as MTF-E, a thirteen-residue, maternally
transmitted minor histocompatibility antigen. The antigenic structure of MTF-E
was unpredictable due to its extraordinary length and two arginines that could
serve as potential anchor residues. The crystal structure of RT1-Aa-MTF-E at
2.55 A shows that both peptide termini are anchored, as in other class I
molecules, but the central residues in two independent pMHC complexes adopt
completely different bulged conformations based on local environment. The MTF-E
epitope is fully exposed within the putative T cell receptor (TCR) footprint.
The flexibility demonstrated by the MTF-E structures illustrates how different
TCRs may be raised against chemically identical, but structurally dissimilar,
pMHC complexes.
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Selected figure(s)
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Figure 3.
Figure 3. MTF-E Hydrogen Bonding in the RT1-A^a Binding
GrooveThe view is looking directly down into the peptide binding
grooves (shown as gray ribbon diagrams) of molecules A (A) and B
(B) with selected side chains and water molecules colored green,
if they maintain closely similar contacts to MTF-E in both
molecules, and colored blue, if they are dissimilar. Peptides
are represented as in Figure 2C. Oxygen atoms are colored red
and nitrogen atoms are colored cyan in both peptide and MHC
molecules. Hydrogen bonds and salt bridges are shown as dotted
lines.
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Figure 4.
Figure 4. The Rat RT1-A^a F PocketHydrogen bonds and salt
bridges between ArgP13 and residues of RT1-A^a molecules A (A)
and B (B) are shown as dotted lines. Coloring is the same as in
Figure 3. The views are from inside the MHC binding groove
looking toward the peptide C terminus.
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The above figures are
reprinted
by permission from Cell Press:
Immunity
(2001,
14,
81-92)
copyright 2001.
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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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M.Herget,
C.Baldauf,
C.Schölz,
D.Parcej,
K.H.Wiesmüller,
R.Tampé,
R.Abele,
and
E.Bordignon
(2011).
Conformation of peptides bound to the transporter associated with antigen processing (TAP).
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Proc Natl Acad Sci U S A,
108,
1349-1354.
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I.K.Macdonald,
M.Harkiolaki,
L.Hunt,
T.Connelley,
A.V.Carroll,
N.D.MacHugh,
S.P.Graham,
E.Y.Jones,
W.I.Morrison,
D.R.Flower,
and
S.A.Ellis
(2010).
MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors.
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PLoS Pathog,
6,
e1001149.
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PDB code:
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N.Blanchard,
T.Kanaseki,
H.Escobar,
F.Delebecque,
N.A.Nagarajan,
E.Reyes-Vargas,
D.K.Crockett,
D.H.Raulet,
J.C.Delgado,
and
N.Shastri
(2010).
Endoplasmic reticulum aminopeptidase associated with antigen processing defines the composition and structure of MHC class I peptide repertoire in normal and virus-infected cells.
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J Immunol,
184,
3033-3042.
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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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K.K.Wynn,
Z.Fulton,
L.Cooper,
S.L.Silins,
S.Gras,
J.K.Archbold,
F.E.Tynan,
J.J.Miles,
J.McCluskey,
S.R.Burrows,
J.Rossjohn,
and
R.Khanna
(2008).
Impact of clonal competition for peptide-MHC complexes on the CD8+ T-cell repertoire selection in a persistent viral infection.
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Blood,
111,
4283-4292.
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PDB codes:
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K.M.Armstrong,
K.H.Piepenbrink,
and
B.M.Baker
(2008).
Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes.
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Biochem J,
415,
183-196.
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M.A.Sherman,
R.M.Goto,
R.E.Moore,
H.D.Hunt,
T.D.Lee,
and
M.M.Miller
(2008).
Mass spectral data for 64 eluted peptides and structural modeling define peptide binding preferences for class I alleles in two chicken MHC-B haplotypes associated with opposite responses to Marek's disease.
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Immunogenetics,
60,
527-541.
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A.W.Purcell,
J.McCluskey,
and
J.Rossjohn
(2007).
More than one reason to rethink the use of peptides in vaccine design.
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Nat Rev Drug Discov,
6,
404-414.
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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.
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Immunity,
27,
885-899.
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PDB codes:
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U.Malhotra,
F.Li,
J.Nolin,
M.Allison,
H.Zhao,
J.I.Mullins,
S.Self,
and
M.J.McElrath
(2007).
Enhanced detection of human immunodeficiency virus type 1 (HIV-1) Nef-specific T cells recognizing multiple variants in early HIV-1 infection.
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J Virol,
81,
5225-5237.
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A.Suri,
J.J.Walters,
M.G.Levisetti,
M.L.Gross,
and
E.R.Unanue
(2006).
Identification of naturally processed peptides bound to the class I MHC molecule H-2Kd of normal and TAP-deficient cells.
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Eur J Immunol,
36,
544-557.
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E.Joly,
and
V.Rouillon
(2006).
The orthology of HLA-E and H2-Qa1 is hidden by their concerted evolution with other MHC class I molecules.
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Biol Direct,
1,
2.
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M.G.Rudolph,
R.L.Stanfield,
and
I.A.Wilson
(2006).
How TCRs bind MHCs, peptides, and coreceptors.
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Annu Rev Immunol,
24,
419-466.
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S.R.Burrows,
J.Rossjohn,
and
J.McCluskey
(2006).
Have we cut ourselves too short in mapping CTL epitopes?
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Trends Immunol,
27,
11-16.
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T.Blicher,
J.S.Kastrup,
L.Ã.˜.Pedersen,
S.Buus,
and
M.Gajhede
(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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Y.Samino,
D.López,
S.Guil,
L.Saveanu,
P.M.van Endert,
and
M.Del Val
(2006).
A long N-terminal-extended nested set of abundant and antigenic major histocompatibility complex class I natural ligands from HIV envelope protein.
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J Biol Chem,
281,
6358-6365.
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D.B.Moody,
D.M.Zajonc,
and
I.A.Wilson
(2005).
Anatomy of CD1-lipid antigen complexes.
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Nat Rev Immunol,
5,
387-399.
|
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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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F.E.Tynan,
S.R.Burrows,
A.M.Buckle,
C.S.Clements,
N.A.Borg,
J.J.Miles,
T.Beddoe,
J.C.Whisstock,
M.C.Wilce,
S.L.Silins,
J.M.Burrows,
L.Kjer-Nielsen,
L.Kostenko,
A.W.Purcell,
J.McCluskey,
and
J.Rossjohn
(2005).
T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I-bound peptide.
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Nat Immunol,
6,
1114-1122.
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PDB code:
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G.B.Stewart-Jones,
K.di Gleria,
S.Kollnberger,
A.J.McMichael,
E.Y.Jones,
and
P.Bowness
(2005).
Crystal structures and KIR3DL1 recognition of three immunodominant viral peptides complexed to HLA-B*2705.
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Eur J Immunol,
35,
341-351.
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PDB codes:
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L.Li,
W.Chen,
and
M.Bouvier
(2005).
A biochemical and structural analysis of genetic diversity within the HLA-A*11 subtype.
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Immunogenetics,
57,
315-325.
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T.Sandalova,
J.Michaëlsson,
R.A.Harris,
J.Odeberg,
G.Schneider,
K.Kärre,
and
A.Achour
(2005).
A structural basis for CD8+ T cell-dependent recognition of non-homologous peptide ligands: implications for molecular mimicry in autoreactivity.
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J Biol Chem,
280,
27069-27075.
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PDB code:
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K.W.Wucherpfennig
(2004).
Presentation of a self-peptide in two distinct conformations by a disease-associated HLA-B27 subtype.
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J Exp Med,
199,
151-154.
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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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S.Ford,
A.Antoniou,
G.W.Butcher,
and
S.J.Powis
(2004).
Competition for access to the rat major histocompatibility complex class I peptide-loading complex reveals optimization of peptide cargo in the absence of transporter associated with antigen processing (TAP) association.
|
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J Biol Chem,
279,
16077-16082.
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V.Apostolopoulos,
and
E.Lazoura
(2004).
Noncanonical peptides in complex with MHC class I.
|
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Expert Rev Vaccines,
3,
151-162.
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M.L.Diegel,
F.Chen,
R.Laus,
T.J.Graddis,
and
D.Vidovic
(2003).
Major histocompatibility complex class I-restricted presentation of protein antigens without prior intracellular processing.
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Scand J Immunol,
58,
1-8.
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M.G.Rudolph,
and
I.A.Wilson
(2002).
The specificity of TCR/pMHC interaction.
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Curr Opin Immunol,
14,
52-65.
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M.G.Rudolph,
J.G.Luz,
and
I.A.Wilson
(2002).
Structural and thermodynamic correlates of T cell signaling.
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Annu Rev Biophys Biomol Struct,
31,
121-149.
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M.Ramos,
I.Alvarez,
L.Sesma,
A.Logean,
D.Rognan,
and
J.A.López de Castro
(2002).
Molecular mimicry of an HLA-B27-derived ligand of arthritis-linked subtypes with chlamydial proteins.
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J Biol Chem,
277,
37573-37581.
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N.Shastri,
S.Schwab,
and
T.Serwold
(2002).
Producing nature's gene-chips: the generation of peptides for display by MHC class I molecules.
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Annu Rev Immunol,
20,
463-493.
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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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P.M.Rudd,
T.Elliott,
P.Cresswell,
I.A.Wilson,
and
R.A.Dwek
(2001).
Glycosylation and the immune system.
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Science,
291,
2370-2376.
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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
