3E3Q

Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.250 

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


Literature

Distinct CDR3 conformations in TCRs determine the level of cross-reactivity for diverse antigens, but not the docking orientation.

Jones, L.L., Colf, L.A., Stone, J.D., Garcia, K.C., Kranz, D.M.

(2008) J Immunol 181: 6255-6264

  • DOI: 10.4049/jimmunol.181.9.6255
  • Primary Citation of Related Structures:  
    3E2H, 3E3Q

  • PubMed Abstract: 

    • T cells are known to cross-react with diverse peptide MHC Ags through their alphabeta TCR. To explore the basis of such cross-reactivity, we examined the 2C TCR that recognizes two structurally distinct ligands, SIY-K(b) and alloantigen QL9-L(d). In this ...

    T cells are known to cross-react with diverse peptide MHC Ags through their alphabeta TCR. To explore the basis of such cross-reactivity, we examined the 2C TCR that recognizes two structurally distinct ligands, SIY-K(b) and alloantigen QL9-L(d). In this study we characterized the cross-reactivity of several high-affinity 2C TCR variants that contained mutations only in the CDR3alpha loop. Two of the TCR lost their ability to cross-react with the reciprocal ligand (SIY-K(b)), whereas another TCR (m67) maintained reactivity with both ligands. Crystal structures of four of the TCRs in complex with QL9-L(d) showed that CDR1, CDR2, and CDR3beta conformations and docking orientations were remarkably similar. Although the CDR3alpha loop of TCR m67 conferred a 2000-fold higher affinity for SIY-K(b), the TCR maintained the same docking angle on QL9-L(d) as the 2C TCR. Thus, CDR3alpha dictated the affinity and level of cross-reactivity, yet it did so without affecting the conserved docking orientation.

    Organizational Affiliation: 

    Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, L-D alpha chain A, B, H, L, P, U, Y, c175Mus musculusMutation(s): 9 
Gene Names: H2-L
Find proteins for P01897 (Mus musculus)
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Go to UniProtKB:  P01897
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
QL9 peptide G, K, O, Q, T, X, b, f9N/AMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor alpha chain V region PHDS58 C, D, I, M, R, V, Z, d109Mus musculusMutation(s): 7 
Gene Names: TRAV9-4
Find proteins for Q5R1C2 (Mus musculus)
Explore Q5R1C2 
Go to UniProtKB:  Q5R1C2
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TCR beta chain E, F, J, N, S, W, a, e111Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.250 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.472α = 90
b = 160.458β = 90
c = 357.159γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description