7KQL

Anti-Tim3 antibody Fab complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Tim-3 mediates T cell trogocytosis to limit antitumor immunity.

Pagliano, O.Morrison, R.M.Chauvin, J.M.Banerjee, H.Davar, D.Ding, Q.Tanegashima, T.Gao, W.Chakka, S.R.DeBlasio, R.Lowin, A.Kara, K.Ka, M.Zidi, B.Amin, R.Raphael, I.Zhang, S.Watkins, S.C.Sander, C.Kirkwood, J.M.Bosenberg, M.Anderson, A.C.Kuchroo, V.K.Kane, L.P.Korman, A.J.Rajpal, A.West, S.M.Han, M.Bee, C.Deng, X.Schebye, X.M.Strop, P.Zarour, H.M.

(2022) J Clin Invest 132

  • DOI: https://doi.org/10.1172/JCI152864
  • Primary Citation of Related Structures:  
    7KQL

  • PubMed Abstract: 

    T cell immunoglobulin mucin domain-containing protein 3 (Tim-3) negatively regulates innate and adaptive immunity in cancer. To identify the mechanisms of Tim-3 in cancer immunity, we evaluated the effects of Tim-3 blockade in human and mouse melanoma. Here, we show that human programmed cell death 1-positive (PD-1+) Tim-3+CD8+ tumor-infiltrating lymphocytes (TILs) upregulate phosphatidylserine (PS), a receptor for Tim-3, and acquire cell surface myeloid markers from antigen-presenting cells (APCs) through transfer of membrane fragments called trogocytosis. Tim-3 blockade acted on Tim-3+ APCs in a PS-dependent fashion to disrupt the trogocytosis of activated tumor antigen-specific CD8+ T cells and PD-1+Tim-3+ CD8+ TILs isolated from patients with melanoma. Tim-3 and PD-1 blockades cooperated to disrupt trogocytosis of CD8+ TILs in 2 melanoma mouse models, decreasing tumor burden and prolonging survival. Deleting Tim-3 in dendritic cells but not in CD8+ T cells impeded the trogocytosis of CD8+ TILs in vivo. Trogocytosed CD8+ T cells presented tumor peptide-major histocompatibility complexes and became the target of fratricide T cell killing, which was reversed by Tim-3 blockade. Our findings have uncovered a mechanism Tim-3 uses to limit antitumor immunity.


  • Organizational Affiliation

    Department of Medicine and UPMC Hillman Cancer Center.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tim3.18 Fab heavy chainA [auth H]234Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tim3.18 Fab light chainB [auth L]215Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatitis A virus cellular receptor 2C [auth T]129Homo sapiensMutation(s): 0 
Gene Names: HAVCR2TIM3TIMD3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDQ0 (Homo sapiens)
Explore Q8TDQ0 
Go to UniProtKB:  Q8TDQ0
PHAROS:  Q8TDQ0
GTEx:  ENSG00000135077 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TDQ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.105α = 90
b = 63.856β = 94.254
c = 66.407γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description