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PDBsum entry 1kjc
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Cell adhesion protein
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PDB id
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1kjc
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References listed in PDB file
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Key reference
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Title
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Molecular model of the n-Terminal receptor-Binding domain of the human cd6 ligand alcam.
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Authors
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J.Bajorath,
M.A.Bowen,
A.Aruffo.
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Ref.
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Protein Sci, 1995,
4,
1644-1647.
[DOI no: ]
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PubMed id
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Abstract
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CD6-ligand interactions have been implicated in the regulation of T-cell
adhesion and activation. CD6 is a member of the scavenger receptor family,
whereas its human ligand (ALCAM) belongs to the immunoglobulin superfamily. The
extracellular region of ALCAM includes five immunoglobulin-like domains. As a
fusion protein, the N-terminal extracellular domain of ALCAM (ALCAMD1) binds
specifically to CD6. We report the construction, assessment, and analysis of a
molecular model of ALCAMD1. The model defines the CDR-analogous loops, the
location of N-linked glycosylation sites, and residues that form the beta-sheet
faces of the immunoglobulin-like domain. Predicted structural characteristics of
the A'GFCC'C" face of the model are consistent with the presence of monomeric
and dimeric forms of ALCAMD1, which has implications for the receptor-ligand
interactions.
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Figure 1.
Fig. 1. Structure-orientedsequencealignmet of ALCAMDI(ALC)
andCD8.The /3-strands of CD8andthecorresponding(predicted)
ALCAMDIP-strandsareunderlined(theA-strandinCD8,predicted
to be absent in ALCAMDl, is notshown).Residuenumbersare
forALCAMDl The predicted CDR-analogous regions in ALCAMDIare
annotated,and IgSF V-set residues are labeled (*). ALCAMDI
loopregionsmodeled by conforationalserchare given in lowercase.
Residuesidentical CD8andALCAMDlandthe mostconservative
replacementsareshowninbold.
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Figure 2.
Fig. 2. tereorepresentationof theALCAMDl A ALCAMDl monomer,backboneshown as a solid ribbon. The
termini (N, C),the faces A'GFCC'C, green; BED, blue), andthe CDR-analogous loops (1-4, yellow) are labeled.
Positionsofpotential N-linked glycosylation sites are colored in magenta. B Possible Fv-like homodier monomers col-
ored in ray and pink, ALCAMDlatthetopand thegraymonoer at thebottom have thesameorientation.
The spatialarrangementofcomplementary negatively charged (red), positively charged (blue), and hydrophobic (gold) resi-
duesthought tobe consistent with Fv-like dimerization (as discussed in he text) can be seen. Modeling methods: For computer
graphics, model building, and energy minimizations, the InsightWDiscover package (version 2.3.0.; Biosym Technologies,
San was used. Loop conformations were modeled by conformational search using COGEN (version ) (Bruccoleri &
Novotny, 1992). For each loop,theconformation minimum solvent-accessible surface within 3 kcal/mol of the energy min-
imum conformation was selected. Side-chain conformations of surface residues were modeled using low-energy side-chain rota-
mers (Ponder & Richards, 1987). Conservative side-chain replacements in core regions were modeled in conformations as similar
as possible tothe originl residue. The initially assembled model was subjected to someminor minimization (until the
RMS ofthe energy function was - 1.5 kcal/mol/A) to relieve stereochemical constraints.This resulted in a cumula-
tive proteinbackbone RMS deviation (of th &strands to thestructuraltemplate)of less than .5 A.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1995,
4,
1644-1647)
copyright 1995.
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Secondary reference #1
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Title
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Cloning, Mapping, And characterization of activated leukocyte-Cell adhesion molecule (alcam), A cd6 ligand.
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Authors
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M.A.Bowen,
D.D.Patel,
X.Li,
B.Modrell,
A.R.Malacko,
W.C.Wang,
H.Marquardt,
M.Neubauer,
J.M.Pesando,
U.Francke.
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Ref.
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J Exp Med, 1995,
181,
2213-2220.
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PubMed id
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