Evidence map›Paper›PMID 39786927›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2025

CryoEM structure of an MHC-I/TAPBPR peptide-bound intermediate reveals the mechanism of antigen proofreading.

Yi Sun, Ruth A Pumroy, Leena Mallik, Apala Chaudhuri, Chloe Wang, Daniel Hwang, Julia N Danon, Kimia Dasteh Goli, Vera Y Moiseenkova-Bell, Nikolaos G Sgourakis

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. Solution mapping of MHC-I:TCR interactions using a minimalistic protein system.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  9. Article
  10. Article
  11. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Yi SunDepartment of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104.
Ruth A Pumroy *Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.ORCID 0000-0002-6200-6083
Leena Mallik *Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104.
Apala ChaudhuriDepartment of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104.
Chloe WangDepartment of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
Daniel HwangDepartment of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104.
Julia N DanonCenter for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.ORCID 0000-0001-6971-6582
Kimia Dasteh GoliCenter for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.
Vera Y Moiseenkova-BellDepartment of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104.ORCID 0000-0002-0589-4053
Nikolaos G SgourakisDepartment of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104.ORCID 0000-0003-3655-3902

Funding

Human Pancreas Analysis Program for Type 1 Diabetes - HPAP-T1DU01DK112217 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI MARK A. ATKINSON, KLAUS H KAESTNER · 2021 to 2026
$46.8M
An integrative structural biology approach to understanding metabolite recognition by cellular receptorsR35GM125034 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI SGOURAKIS, NIKOLAOS · 2017 to 2025
$4.7M
Structure and Function of TRPV channelsR35GM144120 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI Vera Moiseenkova-Bell · 2022 to 2026
$4.2M
Molecular mechanism of antigen editing by Class-I MHC ChaperonesR01AI143997 · NIAID · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI SGOURAKIS, NIKOLAOS · 2019 to 2023
$4.0M
NextGen - CHOPOT2CA278687 · NCI · CHILDREN'S HOSP OF PHILADELPHIA · PI JOHN M MARIS · 2022 to 2026
$2.7M
HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) R01AI143997HHS | NIH | National Institute of General Medical Sciences (NIGMS) R35GM125034HHS | NIH | National Institute of General Medical Sciences (NIGMS) R35GM144120NCI NIH HHS OT2 CA278687NIAID NIH HHS R01 AI143997NIDDK NIH HHS U01 DK112217NIGMS NIH HHS R35 GM125034NIGMS NIH HHS R35 GM144120
6 · The paper itself

Abstract

Class I major histocompatibility complex (MHC-I) proteins play a pivotal role in adaptive immunity by displaying epitopic peptides to CD8+ T cells. The chaperones tapasin and TAPBPR promote the selection of immunogenic antigens from a large pool of intracellular peptides. Interactions of chaperoned MHC-I molecules with incoming peptides are transient in nature, and as a result, the precise antigen proofreading mechanism remains elusive. Here, we leverage a high-fidelity TAPBPR variant and conformationally stabilized MHC-I, to determine the solution structure of the human antigen editing complex bound to a peptide decoy by cryogenic electron microscopy (cryo-EM) at an average resolution of 3.0 Å. Antigen proofreading is mediated by transient interactions formed between the nascent peptide binding groove with the P2/P3 peptide anchors, where conserved MHC-I residues stabilize incoming peptides through backbone-focused contacts. Finally, using our high-fidelity chaperone, we demonstrate robust peptide exchange on the cell surface across multiple clinically relevant human MHC-I allomorphs. Our work has important ramifications for understanding the selection of immunogenic epitopes for T cell screening and vaccine design applications.

Indexed as

Cryoelectron MicroscopyHistocompatibility Antigens Class IPeptidesAntigen PresentationAntigensCD8-Positive T-LymphocytesHumansImmunoglobulinsMembrane ProteinsMembrane Transport ProteinsModels, MolecularMolecular ChaperonesProtein BindingProtein ConformationAntigensHistocompatibility Antigens Class IImmunoglobulinsMembrane ProteinsMembrane Transport ProteinsMolecular ChaperonesPeptidesTAPBPL protein, humanantigen repertoirecryoEMMHC-Imolecular chaperoneNMR

Identifiers

PMID39786927
PMCPMC11745410

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.