{
"cells": [
{
"cell_type": "markdown",
"id": "08a1bdac",
"metadata": {
"language": "markdown"
},
"source": [
"# Example — GILGFVFTL / HLA-A*02:01 and the CDR3β Arg–Ser motif\n",
"\n",
"The influenza M1₅₈₋₆₆ epitope **GILGFVFTL** presented by **HLA-A*02:01** is recognised by a\n",
"strongly biased, public T-cell response built on TRBV19, whose hallmark is a conserved\n",
"**Arg–Ser (RS) motif** in CDR3β. The canonical structure is the **JM22** TCR (PDB **1oga**),\n",
"with CDR3β `ASSSRSSYEQY` — the Arg and the following Ser reach into the peptide.\n",
"\n",
"This public RS motif is documented in **VDJdb** (Shugay M, Bagaev DV, Zvyagin IV, *et al.*,\n",
"*Nucleic Acids Research* 2018;46(D1):D419–D427, https://doi.org/10.1093/nar/gkx760; record\n",
"retrieved from PubMed, PMID 28977646). Here we orient 1oga into the canonical frame and use the\n",
"tcren complementarity maps to show *where* the Arg–Ser residues contact the peptide. The\n",
"structure is read only from the bootstrapped HF `Native2026` set."
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "7aa2908d",
"metadata": {
"execution": {
"iopub.execute_input": "2026-06-16T12:54:12.372086Z",
"iopub.status.busy": "2026-06-16T12:54:12.371923Z",
"iopub.status.idle": "2026-06-16T12:54:17.958131Z",
"shell.execute_reply": "2026-06-16T12:54:17.957664Z"
},
"language": "python"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"python 3.11.15 | tcren 0.1.0\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"peptide=GILGFVFTL CDR3β=ASSSRSSYEQY crossing=83° incident=-14°\n"
]
}
],
"source": [
"# Load the JM22 complex (1oga) from the HF set, type chains (arda), annotate the MHC groove.\n",
"import warnings; warnings.filterwarnings('ignore')\n",
"import sys\n",
"from pathlib import Path\n",
"import numpy as np, polars as pl, matplotlib, matplotlib.pyplot as plt\n",
"import tcren\n",
"from tcren.structure.io import import_structure\n",
"from tcren.annotation import classify_chains\n",
"from tcren.mhc import annotate_mhc\n",
"from tcren.orient import docking_angles\n",
"from tcren.project2d import (project_structure, residue_markup_table, contacts_table,\n",
" ca_contacts_table, pocket_markers, region_pair_contacts)\n",
"from tcren.viz import render_complementarity_map\n",
"from IPython.display import SVG, display\n",
"print('python', sys.version.split()[0], '| tcren', tcren.__version__)\n",
"\n",
"s = import_structure(Path('data/Native2026/1oga.pdb.gz'), pdb_id='1oga')\n",
"classify_chains(s, organism='human'); annotate_mhc(s)\n",
"cdr3b = next(r.sequence for c in s.chains if c.chain_type == 'TRB'\n",
" for r in c.regions if r.region_type == 'CDR3')\n",
"pep = next(c.sequence() for c in s.chains if c.chain_type == 'PEPTIDE')\n",
"ang = docking_angles(s)\n",
"print(f'peptide={pep} CDR3β={cdr3b} crossing={ang.crossing_angle:.0f}° incident={ang.incident_angle:.0f}°')"
]
},
{
"cell_type": "markdown",
"id": "6f4264e9",
"metadata": {
"language": "markdown"
},
"source": [
"## Where does the Arg–Ser motif touch the peptide?"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "93ea9562",
"metadata": {
"execution": {
"iopub.execute_input": "2026-06-16T12:54:17.959673Z",
"iopub.status.busy": "2026-06-16T12:54:17.959559Z",
"iopub.status.idle": "2026-06-16T12:54:17.976935Z",
"shell.execute_reply": "2026-06-16T12:54:17.976557Z"
},
"language": "python"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CDR3β residues contacting the peptide: ['R98', 'S100', 'S99']\n"
]
},
{
"data": {
"text/html": [
"\n",
"
shape: (6, 5)| cdr3b_res | peptide_res | min_dist | contact_type | motif |
|---|
| str | str | f64 | str | bool |
| "S99" | "V6" | 3.09 | "hydrogen_bond" | true |
| "R98" | "F5" | 3.78 | "polar" | true |
| "S100" | "F5" | 3.82 | "polar" | true |
| "S99" | "F5" | 4.03 | "polar" | true |
| "R98" | "F7" | 4.16 | "hydrophobic" | true |
| "R98" | "V6" | 4.84 | "polar" | true |