PDBsum entry 2cii

Immune system/peptide

PDB id: 2cii

Contents

Protein chains

275 a.a. *

99 a.a. *

Ligands

TYR-PRO-ALA-LEU

GOL ×2

Waters ×101

* Residue conservation analysis

PDB id:

2cii

Name:

Immune system/peptide

Title:

The crystal structure of h-2db complexed with a partial peptide epitope suggests an mhc class i assembly-intermediate

Structure:

H-2 class i histocompatibility antigen d-b alpha chain. Chain: a. Fragment: residues 25-299. Synonym: h-2db. Engineered: yes. Beta-2-microglobulin. Chain: b. Synonym: beta2-m. Engineered: yes.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes.

Biol. unit:

Trimer (from PDB file)

Resolution:

2.55Å R-factor: 0.239 R-free: 0.297

Authors:

A.Glithero,J.Tormo,K.Doering,M.Kojima,E.Y.Jones,T.Elliott

Key ref:

A.Glithero et al. (2006). The crystal structure of H-2D(b) complexed with a partial peptide epitope suggests a major histocompatibility complex class I assembly intermediate. J Biol Chem, 281, 12699-12704. PubMed id: 16478731 DOI: 10.1074/jbc.M511683200

Date:

21-Mar-06 Release date: 29-Mar-06

Protein chain

P01899  (HA11_MOUSE) -  H-2 class I histocompatibility antigen, D-B alpha chain from Mus musculus

Seq: 362 a.a.

Struc: 275 a.a.*

Protein chain

P61769  (B2MG_HUMAN) -  Beta-2-microglobulin from Homo sapiens

Seq: 119 a.a.

Struc: 99 a.a.

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

DOI no: 10.1074/jbc.M511683200

J Biol Chem 281:12699-12704 (2006)

PubMed id: 16478731

The crystal structure of H-2D(b) complexed with a partial peptide epitope suggests a major histocompatibility complex class I assembly intermediate.

A.Glithero, J.Tormo, K.Doering, M.Kojima, E.Y.Jones, T.Elliott.

ABSTRACT

In the absence of bound peptide ligands, major histocompatibility complex (MHC) class I molecules are unstable. In an attempt to determine the minimum requirement for peptide-dependent MHC class I stabilization, we have used short synthetic peptides derived from the Sendai virus nucleoprotein epitope (residues 324-332, 1FAPGNYPAL9) to promote its folding in vitro of H-2D(b). We found that H-2D(b) can be stabilized by the pentapeptide 5NYPAL9, which is equivalent to the C-terminal portion of the optimal nonapeptide and includes both the P5 and P9 anchor residues. We have crystallized the complex of the H-2D(b) molecule with the pentamer and determined the structure to show how a quasi-stable MHC class I molecule can be formed by occupancy of a single binding pocket in the peptide-binding groove.

Selected figure(s)

Figure 1.
FIGURE 1. Dose-dependent recovery of H-2D^b molecules from refolding reactions containing increasing concentrations of FAPGNYPAL ( ), FAPGN ( ), NYPAL ( ), or TYQRTRALV (x).

Figure 4.
FIGURE 4. Comparison of peptide conformations in H-2D^b complexes. The structure of NYPAL (green) is shown superposed with the previously reported structures of WT (FAPGNYPAL; blue) and K2G (FAPGS(O-GlcNAc) YPAL; red). For clarity the Ser^5-linked glycan is omitted from the K2G structure.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 12699-12704) copyright 2006.

Figures were selected by an automated process.