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115 a.a.
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117 a.a.
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214 a.a.
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219 a.a.
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* Residue conservation analysis
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PDB id:
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Complex (immunoglobulin/receptor)
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Title:
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Murine t-cell receptor variable domain/fab complex
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Structure:
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Kb5-c20 t-cell antigen receptor. Chain: a. Fragment: fv fragment, variable domain. Synonym: tcr vaplha vbeta domain. Engineered: yes. Other_details: 24 residue link between valpha c-terminus and vbeta n- terminus. Kb5-c20 t-cell antigen receptor. Chain: b.
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Cell: t-cell. Cellular_location: surface. Expressed in: mus musculus. Expression_system_taxid: 10090. Strain: igg2a. Strain: igg2a
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Biol. unit:
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Tetramer (from
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Resolution:
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Authors:
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D.Housset,G.Mazza,C.Gregoire,C.Piras,B.Malissen,J.C.Fontecilla-Camps
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Key ref:
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D.Housset
et al.
(1997).
The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain.
EMBO J,
16,
4205-4216.
PubMed id:
DOI:
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Date:
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06-Apr-97
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Release date:
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08-Apr-98
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PROCHECK
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Headers
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References
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No UniProt id for this chain
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P04214
(TVB6_MOUSE) -
T-cell receptor beta chain V region E1 from Mus musculus
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Seq:
Struc:
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136 a.a.
117 a.a.*
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DOI no:
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EMBO J
16:4205-4216
(1997)
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PubMed id:
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The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain.
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D.Housset,
G.Mazza,
C.Grégoire,
C.Piras,
B.Malissen,
J.C.Fontecilla-Camps.
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ABSTRACT
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The crystal structure of a mouse T-cell antigen receptor (TCR) Fv fragment
complexed to the Fab fragment of a specific anti-clonotypic antibody has been
determined to 2.6 A resolution. The polypeptide backbone of the TCR V alpha
domain is very similar to those of other crystallographically determined V
alphas, whereas the V beta structure is so far unique among TCR V beta domains
in that it displays a switch of the c" strand from the inner to the outer
beta-sheet. The beta chain variable region of this TCR antigen-binding site is
characterized by a rather elongated third complementarity-determining region
(CDR3beta) that packs tightly against the CDR3 loop of the alpha chain, without
leaving any intervening hydrophobic pocket. Thus, the conformation of the CDR
loops with the highest potential diversity distinguishes the structure of this
TCR antigen-binding site from those for which crystallographic data are
available. On the basis of all these results, we infer that a significant
conformational change of the CDR3beta loop found in our TCR is required for
binding to its cognate peptide-MHC ligand.
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Selected figure(s)
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Figure 3.
Figure 3 Stereoscopic view of the KB5-C20 V  -V
 interface.
The V and
V domains
are on the left and right sides, respectively. Only side chains
of residues involved in interdomain interactions are shown.
Residues are colour-coded according to their chemical nature.
Acidic residues are red, basic residues dark blue, polar
residues light blue, hydrophobic residues yellow and aromatic
residues purple.
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Figure 7.
Figure 7 Stereo pairs of the electron density map of the model
contoured at the  level,
and generated from SIGMAA-weighted 2mF[o]-DF[c] coefficients
(Read, 1986). (A) The switched c" strand and the d strand of the
V domain
are shown to illustrate their extended interactions. (B) The
CDR3 loop
is very well defined in the electron density map.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1997,
16,
4205-4216)
copyright 1997.
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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.Xu,
J.C.Pizarro,
M.A.Holmes,
C.McBeth,
V.Groh,
T.Spies,
and
R.K.Strong
(2011).
Crystal structure of a gammadelta T-cell receptor specific for the human MHC class I homolog MICA.
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Proc Natl Acad Sci U S A,
108,
2414-2419.
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PDB code:
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K.Rubtsova,
J.P.Scott-Browne,
F.Crawford,
S.Dai,
P.Marrack,
and
J.W.Kappler
(2009).
Many different Vbeta CDR3s can reveal the inherent MHC reactivity of germline-encoded TCR V regions.
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Proc Natl Acad Sci U S A,
106,
7951-7956.
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|
|
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|
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D.Bandyopadhyay,
and
E.L.Mehler
(2008).
Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment.
|
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Proteins,
72,
646-659.
|
|
|
|
|
|
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E.J.Collins,
and
D.S.Riddle
(2008).
TCR-MHC docking orientation: natural selection, or thymic selection?
|
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Immunol Res,
41,
267-294.
|
|
|
|
|
|
|
J.K.Archbold,
W.A.Macdonald,
S.R.Burrows,
J.Rossjohn,
and
J.McCluskey
(2008).
T-cell allorecognition: a case of mistaken identity or déjà vu?
|
| |
Trends Immunol,
29,
220-226.
|
|
|
|
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|
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Z.Ma,
K.A.Sharp,
P.A.Janmey,
and
T.H.Finkel
(2008).
Surface-anchored monomeric agonist pMHCs alone trigger TCR with high sensitivity.
|
| |
PLoS Biol,
6,
e43.
|
|
|
|
|
|
|
B.Moza,
R.A.Buonpane,
P.Zhu,
C.A.Herfst,
A.K.Rahman,
J.K.McCormick,
D.M.Kranz,
and
E.J.Sundberg
(2006).
Long-range cooperative binding effects in a T cell receptor variable domain.
|
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Proc Natl Acad Sci U S A,
103,
9867-9872.
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|
|
|
|
|
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M.G.Rudolph,
R.L.Stanfield,
and
I.A.Wilson
(2006).
How TCRs bind MHCs, peptides, and coreceptors.
|
| |
Annu Rev Immunol,
24,
419-466.
|
|
|
|
|
|
|
Y.Xin-Sheng,
X.Zheng-Jun,
M.Li,
S.Wan-Bang,
Z.Wei-Yang,
W.Qian,
H.Zhi-Ming,
M.Min-Jie,
L.Ying,
W.Zhen-Qiang,
H.Xiao-Wei,
W.Ju-Fang,
and
W.Xiao-Ning
(2006).
Analysis of the CDR3 region of alpha/beta T-cell receptors (TCRs) and TCR BD gene double-stranded recombination signal sequence breaks end in peripheral blood mononuclear cells of T-lineage acute lymphoblastic leukemia.
|
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Clin Lab Haematol,
28,
405-415.
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|
|
|
|
|
|
H.Li,
S.Van Vranken,
Y.Zhao,
Z.Li,
Y.Guo,
L.Eisele,
and
Y.Li
(2005).
Crystal structures of T cell receptor (beta) chains related to rheumatoid arthritis.
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Protein Sci,
14,
3025-3038.
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PDB codes:
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D.Housset,
and
B.Malissen
(2003).
What do TCR-pMHC crystal structures teach us about MHC restriction and alloreactivity?
|
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Trends Immunol,
24,
429-437.
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R.H.McMahan,
L.Watson,
R.Meza-Romero,
G.G.Burrows,
D.N.Bourdette,
and
A.C.Buenafe
(2003).
Production, characterization, and immunogenicity of a soluble rat single chain T cell receptor specific for an encephalitogenic peptide.
|
| |
J Biol Chem,
278,
30961-30970.
|
|
|
|
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|
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Z.Wang,
and
J.Moult
(2003).
Three-dimensional structural location and molecular functional effects of missense SNPs in the T cell receptor Vbeta domain.
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Proteins,
53,
748-757.
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E.May,
N.Dulphy,
E.Frauendorf,
R.Duchmann,
P.Bowness,
J.A.Lopez de Castro,
A.Toubert,
and
E.Märker-Hermann
(2002).
Conserved TCR beta chain usage in reactive arthritis; evidence for selection by a putative HLA-B27-associated autoantigen.
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Tissue Antigens,
60,
299-308.
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P.Chakrabarti,
and
J.Janin
(2002).
Dissecting protein-protein recognition sites.
|
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Proteins,
47,
334-343.
|
|
|
|
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|
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T.Steiner,
J.T.Kaiser,
S.Marinkoviç,
R.Huber,
and
M.C.Wahl
(2002).
Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities.
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EMBO J,
21,
4641-4653.
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PDB codes:
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D.W.Ritchie,
and
G.J.Kemp
(2000).
Protein docking using spherical polar Fourier correlations.
|
| |
Proteins,
39,
178-194.
|
|
|
|
|
|
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J.Foote,
and
A.Raman
(2000).
A relation between the principal axes of inertia and ligand binding.
|
| |
Proc Natl Acad Sci U S A,
97,
978-983.
|
|
|
|
|
|
|
A.Achour,
R.A.Harris,
K.Persson,
J.Sundbäck,
C.L.Sentman,
G.Schneider,
Y.Lindqvist,
and
K.Kärre
(1999).
Murine class I major histocompatibility complex H-2Dd: expression, refolding and crystallization.
|
| |
Acta Crystallogr D Biol Crystallogr,
55,
260-262.
|
|
|
|
|
|
|
E.L.Reinherz,
K.Tan,
L.Tang,
P.Kern,
J.Liu,
Y.Xiong,
R.E.Hussey,
A.Smolyar,
B.Hare,
R.Zhang,
A.Joachimiak,
H.C.Chang,
G.Wagner,
and
J.Wang
(1999).
The crystal structure of a T cell receptor in complex with peptide and MHC class II.
|
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Science,
286,
1913-1921.
|
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|
PDB code:
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E.P.Grant,
M.Degano,
J.P.Rosat,
S.Stenger,
R.L.Modlin,
I.A.Wilson,
S.A.Porcelli,
and
M.B.Brenner
(1999).
Molecular recognition of lipid antigens by T cell receptors.
|
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J Exp Med,
189,
195-205.
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|
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|
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H.Li,
A.Llera,
E.L.Malchiodi,
and
R.A.Mariuzza
(1999).
The structural basis of T cell activation by superantigens.
|
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Annu Rev Immunol,
17,
435-466.
|
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K.C.Garcia,
L.Teyton,
and
I.A.Wilson
(1999).
Structural basis of T cell recognition.
|
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Annu Rev Immunol,
17,
369-397.
|
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|
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K.C.Garcia
(1999).
Molecular interactions between extracellular components of the T-cell receptor signaling complex.
|
| |
Immunol Rev,
172,
73-85.
|
|
|
|
|
|
|
P.S.Andersen,
P.M.Lavoie,
R.P.Sékaly,
H.Churchill,
D.M.Kranz,
P.M.Schlievert,
K.Karjalainen,
and
R.A.Mariuzza
(1999).
Role of the T cell receptor alpha chain in stabilizing TCR-superantigen-MHC class II complexes.
|
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Immunity,
10,
473-483.
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|
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B.Arden
(1998).
Conserved motifs in T-cell receptor CDR1 and CDR2: implications for ligand and CD8 co-receptor binding.
|
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Curr Opin Immunol,
10,
74-81.
|
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|
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B.C.Sim,
D.Lo,
and
N.R.Gascoigne
(1998).
Preferential expression of TCR V alpha regions in CD4/CD8 subsets: class discrimination or co-receptor recognition?
|
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Immunol Today,
19,
276-282.
|
|
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C.A.Mallick-Wood,
J.M.Lewis,
L.I.Richie,
M.J.Owen,
R.E.Tigelaar,
and
A.C.Hayday
(1998).
Conservation of T cell receptor conformation in epidermal gammadelta cells with disrupted primary Vgamma gene usage.
|
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Science,
279,
1729-1733.
|
|
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|
|
|
G.Mazza,
D.Housset,
C.Piras,
C.Gregoire,
S.Y.Lin,
J.C.Fontecilla-Camps,
and
B.Malissen
(1998).
Glimpses at the recognition of peptide/MHC complexes by T-cell antigen receptors.
|
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Immunol Rev,
163,
187-196.
|
|
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|
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|
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H.Li,
A.Llera,
D.Tsuchiya,
L.Leder,
X.Ysern,
P.M.Schlievert,
K.Karjalainen,
and
R.A.Mariuzza
(1998).
Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B.
|
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Immunity,
9,
807-816.
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PDB code:
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H.Li,
A.Llera,
and
R.A.Mariuzza
(1998).
Structure-function studies of T-cell receptor-superantigen interactions.
|
| |
Immunol Rev,
163,
177-186.
|
|
|
|
|
|
|
J.Wang,
K.Lim,
A.Smolyar,
M.Teng,
J.Liu,
A.G.Tse,
J.Liu,
R.E.Hussey,
Y.Chishti,
C.T.Thomson,
R.M.Sweet,
S.G.Nathenson,
H.C.Chang,
J.C.Sacchettini,
and
E.L.Reinherz
(1998).
Atomic structure of an alphabeta T cell receptor (TCR) heterodimer in complex with an anti-TCR fab fragment derived from a mitogenic antibody.
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EMBO J,
17,
10-26.
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PDB code:
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K.C.Garcia,
and
L.Teyton
(1998).
T-cell receptor peptide-MHC interactions: biological lessons from structural studies.
|
| |
Curr Opin Biotechnol,
9,
338-343.
|
|
|
|
|
|
|
K.C.Garcia,
M.Degano,
L.R.Pease,
M.Huang,
P.A.Peterson,
L.Teyton,
and
I.A.Wilson
(1998).
Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen.
|
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Science,
279,
1166-1172.
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PDB code:
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M.Feng,
D.Chou,
Y.Liaw,
and
M.Lai
(1998).
Conserved T-cell receptor class II major histocompatibility complex contact detected in a T-lymphocyte population.
|
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Immunology,
95,
185-192.
|
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|
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M.M.Davis,
J.J.Boniface,
Z.Reich,
D.Lyons,
J.Hampl,
B.Arden,
and
Y.Chien
(1998).
Ligand recognition by alpha beta T cell receptors.
|
| |
Annu Rev Immunol,
16,
523-544.
|
|
|
|
|
|
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P.J.Fairchild
(1998).
Presentation of antigenic peptides by products of the major histocompatibility complex.
|
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J Pept Sci,
4,
182-194.
|
|
|
|
|
|
|
R.Zamoyska
(1998).
CD4 and CD8: modulators of T-cell receptor recognition of antigen and of immune responses?
|
| |
Curr Opin Immunol,
10,
82-87.
|
|
|
|
|
|
|
T.C.Manning,
C.J.Schlueter,
T.C.Brodnicki,
E.A.Parke,
J.A.Speir,
K.C.Garcia,
L.Teyton,
I.A.Wilson,
and
D.M.Kranz
(1998).
Alanine scanning mutagenesis of an alphabeta T cell receptor: mapping the energy of antigen recognition.
|
| |
Immunity,
8,
413-425.
|
|
|
|
|
|
|
X.Ysern,
H.Li,
and
R.A.Mariuzza
(1998).
Imperfect interfaces.
|
| |
Nat Struct Biol,
5,
412-414.
|
|
|
|
|
|
|
Z.Weng,
and
C.DeLisi
(1998).
Toward a predictive understanding of molecular recognition.
|
| |
Immunol Rev,
163,
251-266.
|
|
|
|
|
|
|
I.A.Wilson,
and
K.C.Garcia
(1997).
T-cell receptor structure and TCR complexes.
|
| |
Curr Opin Struct Biol,
7,
839-848.
|
|
|
|
|
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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
