5E8P

The structure of the TEIPP associated altered peptide ligand Trh4-p5NLE in complex with H-2D(b)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The MHC Class I Cancer-Associated Neoepitope Trh4 Linked with Impaired Peptide Processing Induces a Unique Noncanonical TCR Conformer.

Hafstrand, I., Doorduijn, E.M., Duru, A.D., Buratto, J., Oliveira, C.C., Sandalova, T., van Hall, T., Achour, A.

(2016) J Immunol 196: 2327-2334

  • DOI: 10.4049/jimmunol.1502249
  • Primary Citation of Related Structures:  
    5E8P, 5E8O, 5E8N

  • PubMed Abstract: 

    • MHC class I downregulation represents a significant challenge for successful T cell-based immunotherapy. T cell epitopes associated with impaired peptide processing (TEIPP) constitute a novel category of immunogenic Ags that are selectively presented ...

    MHC class I downregulation represents a significant challenge for successful T cell-based immunotherapy. T cell epitopes associated with impaired peptide processing (TEIPP) constitute a novel category of immunogenic Ags that are selectively presented on transporter associated with Ag processing-deficient cells. The TEIPP neoepitopes are CD8 T cell targets, derived from nonmutated self-proteins that might be exploited to prevent immune escape. In this study, the crystal structure of H-2D(b) in complex with the first identified TEIPP Ag (MCLRMTAVM) derived from the Trh4 protein has been determined to 2.25 Å resolution. In contrast to prototypic H-2D(b) peptides, Trh4 takes a noncanonical peptide-binding pattern with extensive sulfur-π interactions that contribute to the overall complex stability. Importantly, the noncanonical methionine at peptide position 5 acts as a main anchor, altering only the conformation of the H-2D(b) residues Y156 and H155 and thereby forming a unique MHC/peptide conformer that is essential for recognition by TEIPP-specific T cells. Substitution of peptide residues p2C and p5M to the conservative α-aminobutyric acid and norleucine, respectively, significantly reduced complex stability, without altering peptide conformation or T cell recognition. In contrast, substitution of p5M to a conventional asparagine abolished recognition by the H-2D(b)/Trh4-specific T cell clone LnB5. We anticipate that the H-2D(b)/Trh4 complex represents the first example, to our knowledge, of a broader repertoire of alternative MHC class I binders.

    Organizational Affiliation: 

    Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institutet, SE-10450 Stockholm, Sweden; and adnane.achour@ki.se T.van_Hall@lumc.nl.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chainA, D276Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, E99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ceramide synthase 5C, F9Mus musculusMutation(s): 1 
Gene Names: Cers5, Lass5, Trh4
EC: 2.3.1.24 (PDB Primary Data), 2.3.1 (UniProt)
Find proteins for Q9D6K9 (Mus musculus)
Explore Q9D6K9 
Go to UniProtKB:  Q9D6K9
NIH Common Fund Data Resources
IMPC  MGI:1919199
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE		C,FL-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.59α = 90
b = 123.772β = 104.31
c = 97.683γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2016-03-02
    Changes: Database references