PDBsum entry 1e87

Sugar binding protein

PDB id: 1e87

Contents

Protein chain

117 a.a. *

Ligands

GOL

Metals

_ZN

Waters ×108

* Residue conservation analysis

PDB id:

1e87

Name:

Sugar binding protein

Title:

Human cd69 - trigonal form

Structure:

Early activation antigen cd69. Chain: a. Fragment: c-type lectin-like domain, residues 82-199. Synonym: activation inducer molecule, aim, bl-ac/p26, c-type lectin domain family 2 member c, ea1, early t-cell activation antigen p60, gp32/28, leukocyte surface antigen leu-23, mlr-3, cd69, leu-23. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell: hematopoietic cell. Cellular_location: cell surface. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.50Å R-factor: 0.229 R-free: 0.245

Authors:

J.Tormo

Key ref:

A.S.Llera et al. (2001). Crystal structure of the C-type lectin-like domain from the human hematopoietic cell receptor CD69. J Biol Chem, 276, 7312-7319. PubMed id: 11036086 DOI: 10.1074/jbc.M008573200

Date:

18-Sep-00 Release date: 26-Sep-00

Protein chain

Q07108  (CD69_HUMAN) -  Early activation antigen CD69 from Homo sapiens

Seq: 199 a.a.

Struc: 117 a.a.

DOI no: 10.1074/jbc.M008573200

J Biol Chem 276:7312-7319 (2001)

PubMed id: 11036086

Crystal structure of the C-type lectin-like domain from the human hematopoietic cell receptor CD69.

A.S.Llera, F.Viedma, F.Sánchez-Madrid, J.Tormo.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 7312-7319) copyright 2001.

Figures were selected by an automated process.