5E9D

RD-1 Mart-1 High bound to Mart-1 decameric peptide (ELA) in complex with HLA-A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry.

Harris, D.T.Singh, N.K.Cai, Q.Smith, S.N.Vander Kooi, C.W.Procko, E.Kranz, D.M.Baker, B.M.

(2016) Structure 24: 1142-1154

  • DOI: 10.1016/j.str.2016.04.011
  • Primary Citation of Related Structures:  
    5E9D

  • PubMed Abstract: 
  • Utilizing a diverse binding site, T cell receptors (TCRs) specifically recognize a composite ligand comprised of a foreign peptide and a major histocompatibility complex protein (MHC). To help understand the determinants of TCR specificity, we studie ...

    Utilizing a diverse binding site, T cell receptors (TCRs) specifically recognize a composite ligand comprised of a foreign peptide and a major histocompatibility complex protein (MHC). To help understand the determinants of TCR specificity, we studied a parental and engineered receptor whose peptide specificity had been switched via molecular evolution. Altered specificity was associated with a significant change in TCR-binding geometry, but this did not impact the ability of the TCR to signal in an antigen-specific manner. The determinants of binding and specificity were distributed among contact and non-contact residues in germline and hypervariable loops, and included disruption of key TCR-MHC interactions that bias αβ TCRs toward particular binding modes. Sequence-fitness landscapes identified additional mutations that further enhanced specificity. Our results demonstrate that TCR specificity arises from the distributed action of numerous sites throughout the interface, with significant implications for engineering therapeutic TCRs with novel and functional recognition properties.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 1234 Notre Dame Avenue, South Bend, IN 46557, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainAF275Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
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PHAROS  P04439
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBG100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
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PHAROS  P61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Melanoma derived Mart-1 peptideCH10Homo sapiensMutation(s): 0 
Gene Names: MLANAMART1
Find proteins for Q16655 (Homo sapiens)
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PHAROS  Q16655
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
A6-TCR ValphaDI129Homo sapiensMutation(s): 2 
Gene Names: TRAV12-2
Find proteins for A0A075B6T6 (Homo sapiens)
Explore A0A075B6T6 
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PHAROS  A0A075B6T6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
A6-TCR VbetaEJ156Homo sapiensMutation(s): 5 
Gene Names: TRBV6-5
Find proteins for A0A0K0K1A5 (Homo sapiens)
Explore A0A0K0K1A5 
Go to UniProtKB:  A0A0K0K1A5
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PHAROS  A0A0K0K1A5
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.438α = 90
b = 164.484β = 100.56
c = 95.201γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references