PDBsum entry 1kjc

Cell adhesion protein

PDB id: 1kjc

Contents

Protein chain

106 a.a.

Theoretical model

PDB id:

1kjc

Name:

Cell adhesion protein

Title:

Theoretical model of the human cd6 ligand alcam (activated leukocyte-cell adhesion molecule), n-terminal receptor-binding domain

Structure:

Cd6 ligand alcam. Chain: null. Fragment: n-terminal immunoglobulin-like domain. Synonym: activated leukocyte-cell adhesion molecule

Source:

Homo sapiens. Human

Authors:

J.Bajorath,M.A.Bowen,A.Aruffo

Key ref:

J.Bajorath et al. (1995). Molecular model of the N-terminal receptor-binding domain of the human CD6 ligand ALCAM. Protein Sci, 4, 1644-1647. PubMed id: 8520490 DOI: 10.1002/pro.5560040822

Date:

28-Nov-95 Release date: 03-Apr-96

Protein chain

No UniProt id for this chain

Struc: 106 a.a.

DOI no: 10.1002/pro.5560040822

Protein Sci 4:1644-1647 (1995)

PubMed id: 8520490

Molecular model of the N-terminal receptor-binding domain of the human CD6 ligand ALCAM.

J.Bajorath, M.A.Bowen, A.Aruffo.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1995, 4, 1644-1647) copyright 1995.