PDBsum entry 1k8d

Immune system

PDB id: 1k8d

Contents

Protein chains

274 a.a. *

99 a.a. *

Ligands

ILE-LEU-MET-GLU-HIS-ILE-HIS-LYS-LEU

Waters ×273

* Residue conservation analysis

PDB id:

1k8d

Name:

Immune system

Title:

Crystal structure of the non-classical mhc class ib qa-2 complexed with a self peptide

Structure:

Qa-2 antigen. Chain: a. Fragment: extracellular alpha-1, extracellular alpha-2, extracellular alpha-3. Synonym: h-2 class i histocompatibility antigen, q7 alpha chain. Engineered: yes. Beta-2-microglobulin. Chain: b. Engineered: yes.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: q9. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of the peptide is naturally found in mus musculus (mouse).

Biol. unit:

Trimer (from PQS)

Resolution:

2.30Å R-factor: 0.222 R-free: 0.278

Authors:

X.He,P.Tabaczewski,J.Ho,I.Stroynowski,K.C.Garcia

Key ref:

X.He et al. (2001). Promiscuous antigen presentation by the nonclassical MHC Ib Qa-2 is enabled by a shallow, hydrophobic groove and self-stabilized peptide conformation. Structure, 9, 1213-1224. PubMed id: 11738047 DOI: 10.1016/S0969-2126(01)00689-X

Date:

23-Oct-01 Release date: 19-Dec-01

Protein chain

P14429  (HA17_MOUSE) -  H-2 class I histocompatibility antigen, Q7 alpha chain from Mus musculus

Seq: 334 a.a.

Struc: 274 a.a.*

Protein chain

P01887  (B2MG_MOUSE) -  Beta-2-microglobulin from Mus musculus

Seq: 119 a.a.

Struc: 99 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1016/S0969-2126(01)00689-X

Structure 9:1213-1224 (2001)

PubMed id: 11738047

Promiscuous antigen presentation by the nonclassical MHC Ib Qa-2 is enabled by a shallow, hydrophobic groove and self-stabilized peptide conformation.

X.He, P.Tabaczewski, J.Ho, I.Stroynowski, K.C.Garcia.

ABSTRACT

BACKGROUND: Qa-2 is a nonclassical MHC Ib antigen, which has been implicated in both innate and adaptive immune responses, as well as embryonic development. Qa-2 has an unusual peptide binding specificity in that it requires two dominant C-terminal anchor residues and is capable of associating with a substantially more diverse array of peptide sequences than other nonclassical MHC. RESULTS: We have determined the crystal structure, to 2.3 A, of the Q9 gene of murine Qa-2 complexed with a self-peptide derived from the L19 ribosomal protein, which is abundant in the pool of peptides eluted from the Q9 groove. The 9 amino acid peptide is bound high in a shallow, hydrophobic binding groove of Q9, which is missing a C pocket. The peptide makes few specific contacts and exhibits extremely poor shape complementarity to the MHC groove, which facilitates the presentation of a degenerate array of sequences. The L19 peptide is in a centrally bulged conformation that is stabilized by intramolecular interactions from the invariant P7 histidine anchor residue and by a hydrophobic core of preferred secondary anchor residues that have minimal interaction with the MHC. CONCLUSIONS: Unexpectedly, the preferred secondary peptide residues that exhibit tenuous contact with Q9 contribute significantly to the overall stability of the peptide-MHC complex. The structure of this complex implies a "conformational" selection by Q9 for peptide residues that optimally stabilize the large bulge rather than making intimate contact with the MHC pockets.

Selected figure(s)

Figure 3.
Figure 3. Intermolecular Interactions between the L19 Peptide and Q9(a) All-atom representation of the L19 peptide (cyan) and amino acid residues with which it interacts in the Q9 groove. The identity of Q9 residues is indicated, and the A, B, D, E, and F pocket residues of Q9 are colored pink, orange, red, blue, and green, respectively.(b) Two-dimensional planar representation of the interactions between L19 and Q9 in an orientation roughly corresponding to that shown in (a). The peptide is colored cyan, with oxygen atoms red and nitrogen atoms blue.

The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 1213-1224) copyright 2001.

Figure was selected by an automated process.