6UZ1

Noncanonical binding of single-chain A6 TCR variant S3-4 in complex with Tax/HLA-A2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes.

Singh, N.K., Alonso, J.A., Harris, D.T., Anderson, S.D., Ma, J., Hellman, L.M., Rosenberg, A.M., Kolawole, E.M., Evavold, B.D., Kranz, D.M., Baker, B.M.

(2020) Biochemistry 59: 4163-4175

  • DOI: 10.1021/acs.biochem.0c00689
  • Primary Citation of Related Structures:  
    6UZ1

  • PubMed Abstract: 

    • T cell receptors (TCRs) orchestrate cellular immunity by recognizing peptides presented by a range of major histocompatibility complex (MHC) proteins. Naturally occurring TCRs bind the composite peptide/MHC surface, recognizing peptides that are structurally and chemically compatible with the TCR binding site ...

    T cell receptors (TCRs) orchestrate cellular immunity by recognizing peptides presented by a range of major histocompatibility complex (MHC) proteins. Naturally occurring TCRs bind the composite peptide/MHC surface, recognizing peptides that are structurally and chemically compatible with the TCR binding site. Here we describe a molecularly evolved TCR variant that binds the human class I MHC protein HLA-A2 independent of the bound peptide, achieved by a drastic perturbation of the TCR binding geometry that places the molecule far from the peptide binding groove. This unique geometry is unsupportive of normal T cell signaling. A substantial divergence between affinity measurements in solution and in two dimensions between proximal cell membranes leads us to attribute the lack of signaling to steric hindrance that limits binding in the confines of a cell-cell interface. Our results provide an example of how receptor binding geometry can impact T cell function and provide further support for the view that germline-encoded residues in TCR binding loops evolved to drive productive TCR recognition and signaling.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class I antigen, A-2 alpha chainA, D [auth F]275Homo sapiensMutation(s): 0 
Gene Names: HLA-A
Find proteins for A0A140T913 (Homo sapiens)
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Go to UniProtKB:  A0A140T913
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, E [auth G]100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS:  P61769
GTEx:  ENSG00000166710
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
LEU-LEU-PHE-GLY-TYR-PRO-VAL-TYR-VALC, F [auth H]9Homo sapiensMutation(s): 0 
Find proteins for P14079 (Human T-cell leukemia virus 1 (isolate Caribbea HS-35 subtype A))
Explore P14079 
Go to UniProtKB:  P14079
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T cell receptor, alpha chainI [auth D], G [auth I]110Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
T cell receptor, beta chainJ [auth E], H [auth J]115Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES
Download Ideal Coordinates CCD File 
 K [auth B], L [auth F]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 236.65α = 90
b = 236.65β = 90
c = 63.146γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2019-11-14 
  • Released Date: 2020-10-28 
    • Deposition Author(s): Ma, J., Singh, N.K.

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references