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PDBsum entry 1e87
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Sugar binding protein
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PDB id
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1e87
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the c-Type lectin-Like domain from the human hematopoietic cell receptor cd69.
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Authors
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A.S.Llera,
F.Viedma,
F.Sánchez-Madrid,
J.Tormo.
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Ref.
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J Biol Chem, 2001,
276,
7312-7319.
[DOI no: ]
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PubMed id
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Abstract
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CD69, one of the earliest specific antigens acquired during lymphoid activation,
acts as a signal-transducing receptor involved in cellular activation events,
including proliferation and induction of specific genes. CD69 belongs to a
family of receptors that modulate the immune response and whose genes are
clustered in the natural killer (NK) gene complex. The extracellular portion of
these receptors represent a subfamily of C-type lectin-like domains (CTLDs),
which are divergent from true C-type lectins and are referred to as NK-cell
domains (NKDs). We have determined the three-dimensional structure of human CD69
NKD in two different crystal forms. CD69 NKD adopts the canonical CTLD fold but
lacks the features involved in Ca(2+) and carbohydrate binding by C-type
lectins. CD69 NKD dimerizes noncovalently, both in solution and in crystalline
state. The dimer interface consists of a hydrophobic, loosely packed core,
surrounded by polar interactions, including an interdomain beta sheet. The
intersubunit core shows certain structural plasticity that may facilitate
conformational rearrangements for binding to ligands. The surface equivalent to
the binding site of other members of the CTLD superfamily reveals a hydrophobic
patch surrounded by conserved charged residues that probably constitutes the
CD69 ligand-binding site.
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Figure 4.
Fig. 4. The dimerization interface in CD69. A, stereoview
of the dimerization interface in CD69. The two subunits of the
dimer are shown as ribbon diagrams in different colors, yellow
and green. The backbone of strand  0 and side
chains involved in hydrogen bonds or hydrophobic interactions
are represented by ball-and-stick models. Hydrogen bonds are
shown as white broken lines. B, cavity and static disorder at
the dimer interface. A close-up of the hydrophobic cluster at
the dimer interface is shown. The solvent-accessible surface and
the intersubunit cavity, as calculated with program SURFNET
(41), are shown as a semitransparent surface. For the right
subunit, the two alternate conformations for Tyr135 side chain
and the backbone atoms of surrounding residues are shown in
different colors, solid green and semitransparent green. In the
green subunit, strand 0 is shown
as a coil instead of an arrow for clarity.
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Figure 6.
Fig. 6. Surface analysis of the hypothetical
ligand-binding site in CD69. A, representation of the
solvent-accessible surfaces of the ligand-binding site in Ly49A
(left) and the equivalent region in CD69 (right). Surfaces have
been colored based on the nature of the underlying atoms
(carbons and sulfurs in green, polar nitrogens and oxygens in
pink, charged nitrogens in dark blue, and charged oxygens in
red). For Ly49A, the footprinting of its ligand, the mouse MHC
class I molecule H-2D d, has been contoured with a black line.
In CD69, relevant residues in the putative ligand-binding site
have been labeled. B, overview of the CD69 dimer with the region
highlighted in panel A enclosed in a black box.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2001,
276,
7312-7319)
copyright 2001.
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