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PDBsum entry 2coq
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Immune system
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PDB id
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2coq
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References listed in PDB file
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Key reference
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Title
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Structure of a shark ignar antibody variable domain and modeling of an early-Developmental isotype.
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Authors
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V.A.Streltsov,
J.A.Carmichael,
S.D.Nuttall.
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Ref.
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Protein Sci, 2005,
14,
2901-2909.
[DOI no: ]
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PubMed id
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Abstract
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The new antigen receptor (IgNAR) antibodies from sharks are disulphide bonded
dimers of two protein chains, each containing one variable and five constant
domains. Three types of IgNAR variable domains have been discovered, with Type 3
appearing early in shark development and being overtaken by the antigen-driven
affinity-matured Type 1 and 2 response. Here, we have determined the first
structure of a naturally occurring Type 2 IgNAR variable domain, and identified
the disulphide bond that links and stabilizes the CDR1 and CDR3 loops. This
disulphide bridge locks the CDR3 loop in an "upright" conformation in
contrast to other shark antibody structures, where a more lateral configuration
is observed. Further, we sought to model the Type 3 isotype based on the
crystallographic structure reported here. This modeling indicates (1) that
internal Type 3-specific residues combine to pack into a compact immunoglobulin
core that supports the CDR loop regions, and (2) that despite apparent
low-sequence variability, there is sufficient plasticity in the CDR3 loop to
form a conformationally diverse antigen-binding surface.
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Figure 2.
Figure 2. Modeling of the Type 3 IgNAR antibody isotype.
(A) Sequence alignment of Type 3 V[NAR] AAM77191 [GenBank]
with structural templates used for modeling. The conserved Ig
superfamily framework cysteine residues and those found in the
Type 2 and Type 3 CDR3 loop regions are highlighted in yellow.
Regions of sequence homology are highlighted in gray (green,
residues identical in all known V[NAR] structures and AAM77191
[GenBank]
; red, residues conserved in all known V[NAR] structures and
AAM77191 [GenBank]
). (B) The 12A-9 CDR loops shown in C  tube
representation. Side-chain atoms of residues involved in packing
of the hydrophobic core supporting these loops are shown as cpk
balls. Modeled residue side chains for Leu31/Trp31 and
Gly96/Phe96 (as well as Ala66/Phe66) are shown in yellow. (C)
Predicted model of the Type 3 loop in the same representation as
for B. (D) Predicted model of the Type 3 CDR3 loop showing the
conserved central hydrophobic Phe96 residue in yellow,
surrounded by variable residues putatively involved in antigen
binding shown as side-chain atoms rendered as cpk balls. A
solvent accessible surface is also shown in gray, orientation
~170° rotation in the vertical axis. (E) Same as for D, but in
the same orientation as C, and illustrating the relatively small
surface area occupied by the hypervariable residues in the
context of the complete single domain antibody. Diagrams were
constructed in VMD (Humphrey et al. 1996).
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The above figure is
reprinted
by permission from the Protein Society:
Protein Sci
(2005,
14,
2901-2909)
copyright 2005.
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