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 1.2 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: https://doi.org/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 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 Biochemistry, University of Illinois, 600 S. Matthews Ave., Urbana, IL 61801, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain
A, F
275Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
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Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
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UniProt GroupP04439
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Melanoma derived Mart-1 peptide
C, H
10Homo sapiensMutation(s): 0 
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Find proteins for Q16655 (Homo sapiens)
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PHAROS:  Q16655
GTEx:  ENSG00000120215 
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UniProt GroupQ16655
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
A6-TCR Valpha
D, I
129Homo sapiensMutation(s): 2 
Gene Names: TRAV12-2
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Find proteins for A0A075B6T6 (Homo sapiens)
Explore A0A075B6T6 
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PHAROS:  A0A075B6T6
GTEx:  ENSG00000211789 
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UniProt GroupA0A075B6T6
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
A6-TCR Vbeta
E, J
156Homo sapiensMutation(s): 5 
Gene Names: TRBV6-5
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Find proteins for A0A0K0K1A5 (Homo sapiens)
Explore A0A0K0K1A5 
Go to UniProtKB:  A0A0K0K1A5
PHAROS:  A0A0K0K1A5
GTEx:  ENSG00000211721 
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UniProt GroupA0A0K0K1A5
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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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description