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Related Experiment Video

Updated: Jul 12, 2026

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10:09

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Published on: October 1, 2019

TCR-FramePose: a local-frame representation for decomposing global docking and CDR3 loop geometry in TCR-pMHC

Kun Hee Kim, Xianli Jiang, Qing Ye

    Biorxiv : the Preprint Server for Biology
    |July 10, 2026
    PubMed
    Summary

    TCR-FramePose offers a new way to describe T cell receptor structures, improving our understanding of how they bind to peptide-MHC complexes. This method captures detailed geometry, enhancing TCR-pMHC analysis and engineering.

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    Last Updated: Jul 12, 2026

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    Measuring TCR-pMHC Binding In Situ using a FRET-based Microscopy Assay
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    Measuring TCR-pMHC Binding In Situ using a FRET-based Microscopy Assay

    Published on: October 30, 2015

    Area of Science:

    • Structural Biology
    • Immunology
    • Computational Biology

    Background:

    • T cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes is crucial for adaptive immunity.
    • Current methods often oversimplify TCR-pMHC docking geometry, limiting detailed structural comparisons, especially for the CDR3 regions.

    Purpose of the Study:

    • To introduce TCR-FramePose, a novel local-frame descriptor set for quantifying TCR-pMHC complex geometry.
    • To provide a more detailed and comparable geometric representation of TCR-pMHC interactions.

    Main Methods:

    • Developed TCR-FramePose, a descriptor set representing TCR-pMHC complexes as three bodies (TCR, CDR3α, CDR3β) relative to a pMHC groove frame.
    • Analyzed 378 αβTCR-pMHC crystal structures using FramePose, decomposing pose into reach, offset direction, and orientation.
    • Mapped these components to 18 coordinates per complex for tangent-space analyses.

    Main Results:

    • FramePose successfully identified known class-associated differences and revealed subtle whole-TCR and CDR3β orientation shifts.
    • It distinguished distinct binding modes like reverse-polarity and off-axis outliers.
    • FramePose provided nonredundant information on binding affinity and association, particularly from CDR3 orientation, and revealed germline V-region framework as the primary determinant of pose.

    Conclusions:

    • TCR-FramePose offers a comprehensive geometric description of TCR-pMHC interactions, linking germline framework, CDR3-local pose, and interface organization.
    • It serves as a valuable tool for in silico modeling and structure-guided TCR engineering.
    • The descriptor set enhances understanding of TCR-pMHC recognition beyond sequence and energy-based methods.