PDBsum entry: 1cd1

Cd1

PDB id: 1cd1

Contents

Protein chains

273 a.a. *

99 a.a. *

* Residue conservation analysis

PDB id:

1cd1

Name:

Cd1

Title:

Cd1(mouse) antigen presenting molecule

Structure:

Cd1. Chain: a, c. Fragment: alpha1, alpha2, alpha3, beta2-microglobulin. Synonym: mcd1d.1. Engineered: yes. Cd1. Chain: b, d. Fragment: alpha1, alpha2, alpha3, beta2-microglobulin. Synonym: mcd1d.1.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Strain: c57bl/6. Cell_line: sc2. Cell: cortical thymocytes, dendritic cells. Cellular_location: extracellular. Gene: cd1.1. Expressed in: drosophila melanogaster.

Biol. unit:

Monomer (from PDB file)

Resolution:

2.67Å R-factor: 0.192 R-free: 0.330

Authors:

Z.H.Zeng,B.W.Segelke,I.A.Wilson

Key ref:

Z.Zeng et al. (1997). Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove. Science, 277, 339-345. PubMed id: 9219685 DOI: 10.1126/science.277.5324.339

Date:

02-Apr-97 Release date: 15-Oct-97

Protein chains

P11609  (CD1D1_MOUSE) -  Antigen-presenting glycoprotein CD1d1

Seq: 336 a.a.

Struc: 273 a.a.*

Protein chains

P01887  (B2MG_MOUSE) -  Beta-2-microglobulin

Seq: 119 a.a.

Struc: 99 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (13 terms)
• Biological process: immune response (18 terms)
• Biochemical function: protein binding (2 terms)

DOI no: 10.1126/science.277.5324.339

Science 277:339-345 (1997)

PubMed id: 9219685

Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove.

Z.Zeng, A.R.Castaño, B.W.Segelke, E.A.Stura, P.A.Peterson, I.A.Wilson.

ABSTRACT

CD1 represents a third lineage of antigen-presenting molecules that are distantly related to major histocompatibility complex (MHC) molecules in the immune system. The crystal structure of mouse CD1d1, corresponding to human CD1d, at 2.8 resolution shows that CD1 adopts an MHC fold that is more closely related to that of MHC class I than to that of MHC class II. The binding groove, although significantly narrower, is substantially larger because of increased depth and it has only two major pockets that are almost completely hydrophobic. The extreme hydrophobicity and shape of the binding site are consistent with observations that human CD1b and CD1c can present mycobacterial cell wall antigens, such as mycolic acid and lipoarabinomannans. However, mouse CD1d1 can present very hydrophobic peptides, but must do so in a very different way from MHC class Ia and class II molecules.

Selected figure(s)

Figure 4.
Fig. 4. Comparison of molecular surfaces of the binding grooves. The cut away molecular surface (37) of six MHC or MHC-like molecules are shown with electrostatic potentials mapped to their surface. The ligand binding pocket of Maize nonspecific lipid binding protein with palmitic acid bound is also shown for comparison. The groove^ molecular surface of CD1, like that of H-2M3 and nonspecific lipid^ binding protein, is mostly neutral and hydrophobic compared to the grooves of the other MHC molecules or to FcRn. CD1 has by far the largest and deepest groove of all molecules represented^ (37) (pocket A is approximately the same size (in surface area) as the entire binding site of nonspecific lipid binding protein). Many of the specificity pockets present in class I molecules have^ merged to form only two very large pockets in CD1. In FcRn (22), there is essentially no groove. The peptide specificity pockets are labeled A to F for class I (5) and P1-P9 (35) for class II (23) molecules. The FcRn is labeled to show the corresponding location of pockets in class I and is not intended to indicate^ binding pockets. Electrostatics potentials were calculated in GRASP (52) with full formal charge. Positive potential ( 15^ mV) is colored blue, neutral potential (0 mV) is colored green, and negative potential ( 10 mV) is colored red.

Figure 5.
Fig. 5. Residues contributing to the CD1 binding groove. The C trace of mCD1d1 1 2 domains and labeled side chains of residues making up the groove molecular surface (37) shown looking into the^ ligand binding groove. Most of the residues contributing to the^ groove are hydrophobic. The C trace is in purple tubes, carbon side chain atoms in green, nitrogen atoms in blue, oxygen atoms in red, and sulfur atoms in yellow. This figure was generated^ with MIDAS (51).

The above figures are reprinted by permission from the AAAs: Science (1997, 277, 339-345) copyright 1997.

Figures were selected by the author.