PDBsum entry 1ed3

Immune system

PDB id: 1ed3

Contents

Protein chains

275 a.a. *

99 a.a. *

13 a.a. *

Waters ×139

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Two different, Highly exposed, Bulged structures for an unusually long peptide bound to rat mhc class i rt1-Aa.

Authors

J.A.Speir, J.Stevens, E.Joly, G.W.Butcher, I.A.Wilson.

Ref.

Immunity, 2001, 14, 81-92. [DOI no: 10.1016/S1074-7613(01)00091-7]

PubMed id

11163232

Abstract

The rat MHC class Ia molecule RT1-Aa has the unusual capacity to bind long peptides ending in arginine, such as MTF-E, a thirteen-residue, maternally transmitted minor histocompatibility antigen. The antigenic structure of MTF-E was unpredictable due to its extraordinary length and two arginines that could serve as potential anchor residues. The crystal structure of RT1-Aa-MTF-E at 2.55 A shows that both peptide termini are anchored, as in other class I molecules, but the central residues in two independent pMHC complexes adopt completely different bulged conformations based on local environment. The MTF-E epitope is fully exposed within the putative T cell receptor (TCR) footprint. The flexibility demonstrated by the MTF-E structures illustrates how different TCRs may be raised against chemically identical, but structurally dissimilar, pMHC complexes.

Figure 3.
Figure 3. MTF-E Hydrogen Bonding in the RT1-A^a Binding GrooveThe view is looking directly down into the peptide binding grooves (shown as gray ribbon diagrams) of molecules A (A) and B (B) with selected side chains and water molecules colored green, if they maintain closely similar contacts to MTF-E in both molecules, and colored blue, if they are dissimilar. Peptides are represented as in Figure 2C. Oxygen atoms are colored red and nitrogen atoms are colored cyan in both peptide and MHC molecules. Hydrogen bonds and salt bridges are shown as dotted lines.

Figure 4.
Figure 4. The Rat RT1-A^a F PocketHydrogen bonds and salt bridges between ArgP13 and residues of RT1-A^a molecules A (A) and B (B) are shown as dotted lines. Coloring is the same as in Figure 3. The views are from inside the MHC binding groove looking toward the peptide C terminus.

The above figures are reprinted by permission from Cell Press: Immunity (2001, 14, 81-92) copyright 2001.

Secondary reference #1

Title

Identification of the rat maternally transmitted minor histocompatibility antigen.

Authors

P.K.Bhuyan, L.L.Young, K.F.Lindahl, G.W.Butcher.

Ref.

J Immunol, 1997, 158, 3753-3760.

PubMed id

9103440

Secondary reference #2

Title

Efficient generation of major histocompatibility complex class i-Peptide complexes using synthetic peptide libraries.

Authors

J.Stevens, K.H.Wiesmüller, P.J.Barker, P.Walden, G.W.Butcher, E.Joly.

Ref.

J Biol Chem, 1998, 273, 2874-2884. [DOI no: 10.1074/jbc.273.5.2874]

PubMed id

9446598

Figure 4.
Fig. 4. SDS-PAGE analysis for the purification of RT1-A^a heavy chain expressed in E. coli. Heavy chain was expressed as inclusion bodies and purified with Ni-NTA-Sepharose. Stepwise pH-dependent elution allowed separation of monomers (pH 5.9) and multimers (pH 4.5).

Figure 8.
Fig. 8. Comparison of hydrophobic residues for RT1-A^a, RT1-A^u, and RT1-A1^c. Computer-generated models of the three RT1-A molecules used^ in this study. Sequences for residues 1-180 were submitted to the Swiss Model server (49-51). Returned theoretical structures were then edited to remove the 3 domains and displayed using the freeware program Rasmol. Hydrophobic residues (Ala, Leu, Val, Ile, Pro, Phe, Met, and Trp) are displayed as black areas. The^ circled area on each molecule shows the major differences for hydrophobicity.

The above figures are reproduced from the cited reference with permission from the ASBMB

Secondary reference #3

Title

Peptide length preferences for rat and mouse mhc class i molecules using random peptide libraries.

Authors

J.Stevens, K.H.Wiesmüller, P.Walden, E.Joly.

Ref.

Eur J Immunol, 1998, 28, 1272-1279.

PubMed id

9565367

Secondary reference #4

Title

The rat cim effect: tap allele-Dependent changes in a class i mhc anchor motif and evidence against c-Terminal trimming of peptides in the er.

Authors

S.J.Powis, L.L.Young, E.Joly, P.J.Barker, L.Richardson, R.P.Brandt, C.J.Melief, J.C.Howard, G.W.Butcher.

Ref.

Immunity, 1996, 4, 159-165. [DOI no: 10.1016/S1074-7613(00)80680-9]

PubMed id

8624806

Figure 1.
Figure 1. In Vitro Peptide Binding to RT1.A^a Expressed on RMA-S CellsThe large increase in the frequency of Arg at position 9 indicates that peptides with C-terminal Arg residues are strongly favored for binding by RT1.A^a. The panels show the observed frequency of each amino acid in the 642 9-mer peptide set tested (open bars), compared with the top 50 binding peptides (closed bars) as determined by flow cytometry.

Figure 4.
Figure 4. Pulse–Chase Analysis of Site-Directed Mutants of RT1.A^aIn TAP2A cells (rat 2 cells, top left panel) the RT1.A^a heavy chain displays rapid glycan maturation, whereas in TAP2B cells (BN leukemia, top middle panel) the heavy chain matures slowly. Modification of negatively charged residues in the C-terminal binding pocket relieves the retention phenotype in TAP2B cells as shown in the bottom three panels. The fast maturation of wild-type RT1.A^u in TAP2B cells is illustrated in the top right panel.Wild-type RT1.A^u, RT1.A^a, and the indicated mutagenized variants of the RT1.A^a peptide C-terminal binding pocket were immunoprecipitated from ^35S-labeled cells at chase timepoints of 0, 30, and 90 min. The first track of each panel represents precipitation in the presence of an irrelevant anti-class I MAb. Only the heavy chain is shown, but in all instances β2-microglobulin coprecipitated with the heavy chain.

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #5

Title

An analysis of the antigen binding site of rt1.Aa suggests an allele-Specific motif.

Authors

C.J.Thorpe, D.S.Moss, S.J.Powis, J.C.Howard, G.W.Butcher, P.J.Travers.

Ref.

Immunogenetics, 1995, 41, 329-331.

PubMed id

7721357