PDBsum entry 1z0y

Sugar binding protein

PDB id: 1z0y

Contents

Protein chains

314 a.a.

Theoretical model

PDB id:

1z0y

Name:

Sugar binding protein

Title:

Theoretical model of dc-signr ectodomain tetramer

Structure:

Cd209 antigen-like protein 1. Chain: a, b, c, d. Fragment: model tetramer dc-signr. Synonym: dendritic cell-specific icam-3-grabbing nonintegrin 2, dc-sign2, dc-sign related protein, dc-signr, liver/lymph node-specific icam-3-grabbing nonintegrin, l- sign. Engineered: yes

Source:

Homo sapiens. Human. Gene: cd209l, cd209l1

Authors:

G.A.Snyder,M.Colonna,P.D.Sun

Key ref:

G.A.Snyder et al. (2005). The structure of DC-SIGNR with a portion of its repeat domain lends insights to modeling of the receptor tetramer. J Mol Biol, 347, 979-989. PubMed id: 15784257 DOI: 10.1016/j.jmb.2005.01.063

Date:

02-Mar-05 Release date: 19-Apr-05

Protein chains

Q9H8F0  (209L_HUMAN) -

DOI no: 10.1016/j.jmb.2005.01.063

J Mol Biol 347:979-989 (2005)

PubMed id: 15784257

The structure of DC-SIGNR with a portion of its repeat domain lends insights to modeling of the receptor tetramer.

G.A.Snyder, M.Colonna, P.D.Sun.

ABSTRACT

The dendritic cell-specific ICAM-3 non-integrin (DC-SIGN) and its close relative DC-SIGNR recognize various glycoproteins, both pathogenic and cellular, through the receptor lectin domain-mediated carbohydrate recognition. While the carbohydrate-recognition domains (CRD) exist as monomers and bind individual carbohydrates with low affinity and are permissive in nature, the full-length receptors form tetramers through their repeat domain and recognize specific ligands with high affinity. To understand the tetramer-based ligand binding avidity, we determined the crystal structure of DC-SIGNR with its last repeat region. Compared to the carbohydrate-bound CRD structure, the structure revealed conformational changes in the calcium and carbohydrate coordination loops of CRD, an additional disulfide bond between the N and the C termini of the CRD, and a helical conformation for the last repeat. On the basis of the current crystal structure and other published structures with sequence homology to the repeat domain, we generated a tetramer model for DC-SIGN/R using homology modeling and propose a ligand-recognition index to identify potential receptor ligands.

Selected figure(s)

Figure 2.
Figure 2. Carbohydrate-binding and calcium-binding sites. (a) C^a traces of the DC-SIGNR R8 (blue) and DC-SIGNR CRD (gray) primary calcium-binding sites showing side-chains involved in coordinating calcium. In the absence of carbohydrate, Asp377 is not involved in calcium coordination. The calcium ion, seen in nearly the same position in both structures is shown in yellow (Ca2). A water molecule (red) is present in the location where normally ligand binds (DC-SIGNR R8 structure). (b) The secondary calcium-binding site shows the C^a loop in DCSIGNR R8 and DC-SIGNR CRD Loop movement is observed between ligand-bound and apo structures from closed to open, respectively. Calcium ions present in the structure of DC-SIGNR CRD only are shown in gray (Ca1 and Ca3). Side-chain movements between each structure are summarized in Table 2.

Figure 4.
Figure 4. Model of the extracellular portion of the DC-SIGN/R tetramer. (a) A side-view of the model tetramer. The boundary of the repeat domain, CRD and carbohydrate (from DC-SIGNR CRD PDB code 1K9J) are shown as well as a view of the model looking down onto the top of the tetramer. (b) A single helical tetramer model is shown with helical breaks in the region near proline residues.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 347, 979-989) copyright 2005.

Figures were selected by an automated process.