PDBsum entry 1kj3

Immune system

PDB id: 1kj3

Contents

Protein chains

279 a.a. *

99 a.a. *

Ligands

LYS-VAL-ILE-THR-PHE-ILE-ASP-LEU ×2

Waters ×376

* Residue conservation analysis

PDB id:

1kj3

Name:

Immune system

Title:

Mhc class i h-2kb molecule complexed with pkb1 peptide

Structure:

H-2kb mhc class i molecule alpha chain. Chain: h, i. Fragment: extracellular domains (alpha1, alpha2, alpha3). Synonym: h-2kb mhc class i molecule heavy chain. Engineered: yes. Naturally processed octapeptide pkb1. Chain: p, q. Engineered: yes. Beta-2 microglobulin.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: sequence naturally occurs in mus muculus.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.30Å R-factor: 0.211 R-free: 0.259

Authors:

J.-B.Reiser,C.Gregoire,C.Darnault,T.Mosser,A.Guimezanes,A.-M.Schmitt- Verhulst,J.C.Fontecilla-Camps,G.Mazza,B.Malissen,D.Housset

Key ref:

J.B.Reiser et al. (2002). A T cell receptor CDR3beta loop undergoes conformational changes of unprecedented magnitude upon binding to a peptide/MHC class I complex. Immunity, 16, 345-354. PubMed id: 11911820 DOI: 10.1016/S1074-7613(02)00288-1

Date:

04-Dec-01 Release date: 27-Mar-02

Protein chains

P01901  (HA1B_MOUSE) -  H-2 class I histocompatibility antigen, K-B alpha chain from Mus musculus

Seq: 369 a.a.

Struc: 279 a.a.*

Protein chains

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/S1074-7613(02)00288-1

Immunity 16:345-354 (2002)

PubMed id: 11911820

A T cell receptor CDR3beta loop undergoes conformational changes of unprecedented magnitude upon binding to a peptide/MHC class I complex.

J.B.Reiser, C.Grégoire, C.Darnault, T.Mosser, A.Guimezanes, A.M.Schmitt-Verhulst, J.C.Fontecilla-Camps, G.Mazza, B.Malissen, D.Housset.

ABSTRACT

The elongated complementary-determining region (CDR) 3beta found in the unliganded KB5-C20 TCR protrudes from the antigen binding site and prevents its docking onto the peptide/MHC (pMHC) surface according to a canonical diagonal orientation. We now present the crystal structure of a complex involving the KB5-C20 TCR and an octapeptide bound to the allogeneic H-2K(b) MHC class I molecule. This structure reveals how a tremendously large CDR3beta conformational change allows the KB5-C20 TCR to adapt to the rather constrained pMHC surface and achieve a diagonal docking mode. This extreme case of induced fit also shows that TCR plasticity is primarily restricted to CDR3 loops and does not propagate away from the antigen binding site.

Selected figure(s)

Figure 1.
Figure 1. Structure of the KB5-C20/pKB1/H-2K^b ComplexBackbone ribbon representation of the ternary complex showing the overall orientation of the KB5-C20 scFv TCR onto pKB1 bound to the H-2K^b MHC molecule. Domains are color coded as follows: TCR Vα, light red; TCR Vβ, light blue; H-2K^b α1 domain, green; H-2K^b α2 domain, light purple; H-2K^b α3 domain, pink; β2-microglobulin, dark purple. The CDR1 and CDR2 loops from both V domains are drawn as green and red coils, respectively. CDR3α is depicted in dark blue, and CDR3β in light blue. The pKB1 is shown in yellow and in a ball-and-stick format, with the N-terminal end on the left and C-terminal end on the right. Only one of the two complexes in the asymmetric unit of the crystal is shown. Also shown is the carbohydrate chain that could be modeled at the Asn^21α glycosylation site.

Figure 5.
Figure 5. Stereoscopic View of the Peptide Binding Groove of the pKB1/H-2K^b Binary ComplexThe pKB1 peptide is represented as a thick yellow tube, the H-2K^b α1 domain in green, and the H-2K^b α2 domain in purple. Hydrogen bonds involving MHC residue Lys^66kb are likely to play a role in allorecognition and are shown as dotted lines. MHC residues forming the Phe^5p binding pocket are represented in ball-and-stick format. The side chains of H-2K^k molecule have been modeled for positions 66 (Ile) and 97 (Arg) and are shown in orange ball-and-stick format. The latter position is likely to determine in part the peptide binding specificity of H-2K^b and H-2K^k molecules. As exemplified in the present model, peptides, which like pKB1 have large side chain at position P5, will collide with Arg^97kk and thus be excluded from the repertoire of peptides binding to H-2K^k.

The above figures are reprinted by permission from Cell Press: Immunity (2002, 16, 345-354) copyright 2002.

Figures were selected by an automated process.