PDBsum entry 2f53

Immune system

PDB id: 2f53

Contents

Protein chains

275 a.a. *

100 a.a. *

193 a.a. *

243 a.a. *

Ligands

SER-LEU-LEU-MET-TRP-ILE-THR-GLN-CYS

GOL ×4

Metals

_NA

Waters ×728

* Residue conservation analysis

PDB id:

2f53

Name:

Immune system

Title:

Directed evolution of human t-cell receptor cdr2 residues by phage display dramatically enhances affinity for cognate peptide-mhc without apparent cross-reactivity

Structure:

Hla class i histocompatibility antigen. Chain: a. Fragment: extracellular domains alpha 1, alpha2 and alpha3, residues 25-299. Synonym: mhc class i antigen a 2. Engineered: yes. Beta-2-microglobulin. Chain: b. Fragment: beta-2 microglobulin, residues 21-119.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: this sequence occurs naturally in homo sapiens (humans).

Biol. unit:

Pentamer (from PQS)

Resolution:

2.10Å R-factor: 0.169 R-free: 0.231

Authors:

P.J.Rizkallah,B.K.Jakobsen,S.M.Dunn,M.Sami

Key ref:

S.M.Dunn et al. (2006). Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity. Protein Sci, 15, 710-721. PubMed id: 16600963 DOI: 10.1110/ps.051936406

Date:

25-Nov-05 Release date: 25-Apr-06

Protein chain

P04439  (1A03_HUMAN) -  HLA class I histocompatibility antigen, A alpha chain from Homo sapiens

Seq: 365 a.a.

Struc: 275 a.a.*

Protein chain

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

Seq: 119 a.a.

Struc: 100 a.a.*

Protein chain

P01848  (TCA_HUMAN) -  T cell receptor alpha chain constant from Homo sapiens

Seq: 140 a.a.

Struc: 193 a.a.*

Protein chain

No UniProt id for this chain

Struc: 243 a.a.

* PDB and UniProt seqs differ at 22 residue positions (black crosses)

DOI no: 10.1110/ps.051936406

Protein Sci 15:710-721 (2006)

PubMed id: 16600963

Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity.

S.M.Dunn, P.J.Rizkallah, E.Baston, T.Mahon, B.Cameron, R.Moysey, F.Gao, M.Sami, J.Boulter, Y.Li, B.K.Jakobsen.

ABSTRACT

The mammalian alpha/beta T cell receptor (TCR) repertoire plays a pivotal role in adaptive immunity by recognizing short, processed, peptide antigens bound in the context of a highly diverse family of cell-surface major histocompatibility complexes (pMHCs). Despite the extensive TCR-MHC interaction surface, peptide-independent cross-reactivity of native TCRs is generally avoided through cell-mediated selection of molecules with low inherent affinity for MHC. Here we show that, contrary to expectations, the germ line-encoded complementarity determining regions (CDRs) of human TCRs, namely the CDR2s, which appear to contact only the MHC surface and not the bound peptide, can be engineered to yield soluble low nanomolar affinity ligands that retain a surprisingly high degree of specificity for the cognate pMHC target. Structural investigation of one such CDR2 mutant implicates shape complementarity of the mutant CDR2 contact interfaces as being a key determinant of the increased affinity. Our results suggest that manipulation of germ line CDR2 loops may provide a useful route to the production of high-affinity TCRs with therapeutic and diagnostic potential.

Selected figure(s)

Figure 3.
Structural depiction of the CDR2 mutant interactions in the c49c50 --pMHC complex. (A) The CDR2[beta] loop mutations (GAGI to SVGM). The 2BNR model is depicted in red; the c49c50 TCR is colored by atom type, mostly green; the c49c50 MHC is mostly red. Dotted lines indicate contacts between mutated side chains and MHC residues. (B) The CDR2[alpha] loop mutations (QSS to PFW): Q155 of the MHC is pushed deeper into the pocket by the close approach of F51, while W52 forces a tighter packing of the CDR1[alpha] Y30 against W5 of the peptide. The 2BNR MHC is red and the c49c50 TCRa is mostly orange. The figures were prepared using PyMOL (DeLano 2002).

Figure 4.
Electron density contoured at 2[sigma] around the identified metal site (black) in the peptide binding groove of the MHC. Some of the approach contacts are indicated. MHC residues are blue. The bound peptide is yellow. TCR [alpha] and [beta] chain residues are orange and green, respectively. Water molecules are displayed as purple spheres. The figure was generated using PyMOL (DeLano 2002).

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2006, 15, 710-721) copyright 2006.

Figures were selected by an automated process.