2J8U

Large CDR3a loop alteration as a function of MHC mutation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Single MHC mutation eliminates enthalpy associated with T cell receptor binding.

Miller, P.J.Pazy, Y.Conti, B.Riddle, D.Appella, E.Collins, E.J.

(2007) J Mol Biol 373: 315-327

  • DOI: 10.1016/j.jmb.2007.07.028
  • Primary Citation of Related Structures:  
    2UWE, 2JCC, 2J8U

  • PubMed Abstract: 
  • The keystone of the adaptive immune response is T cell receptor (TCR) recognition of peptide presented by major histocompatibility complex (pMHC) molecules. The crystal structure of AHIII TCR bound to MHC, HLA-A2, showed a large interface with an aty ...

    The keystone of the adaptive immune response is T cell receptor (TCR) recognition of peptide presented by major histocompatibility complex (pMHC) molecules. The crystal structure of AHIII TCR bound to MHC, HLA-A2, showed a large interface with an atypical binding orientation. MHC mutations in the interface of the proteins were tested for changes in TCR recognition. From the range of responses observed, three representative HLA-A2 mutants, T163A, W167A, and K66A, were selected for further study. Binding constants and co-crystal structures of the AHIII TCR and the three mutants were determined. K66 in HLA-A2 makes contacts with both peptide and TCR, and has been identified as a critical residue for recognition by numerous TCR. The K66A mutation resulted in the lowest AHIII T cell response and the lowest binding affinity, which suggests that the T cell response may correlate with affinity. Importantly, the K66A mutation does not affect the conformation of the peptide. The change in affinity appears to be due to a loss in hydrogen bonds in the interface as a result of a conformational change in the TCR complementarity-determining region 3 (CDR3) loop. Isothermal titration calorimetry confirmed the loss of hydrogen bonding by a large loss in enthalpy. Our findings are inconsistent with the notion that the CDR1 and CDR2 loops of the TCR are responsible for MHC restriction, while the CDR3 loops interact solely with the peptide. Instead, we present here an MHC mutation that does not change the conformation of the peptide, yet results in an altered conformation of a CDR3.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainAH275Homo sapiensMutation(s): 1 
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-microglobulinBI100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
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Go to UniProtKB:  P61769
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PHAROS  P61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SELF-PEPTIDE P1049CJ9Homo sapiensMutation(s): 0 
Gene Names: EMC7C11orf3C15orf24HT022UNQ905/PRO1926
Find proteins for Q9NPA0 (Homo sapiens)
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Go to UniProtKB:  Q9NPA0
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PHAROS  Q9NPA0
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AHIII TCR ALPHA CHAINEL194Mus musculusMutation(s): 0 
Gene Names: Tcra
Find proteins for P01849 (Mus musculus)
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Go to UniProtKB:  P01849
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
AHIII TCR BETA CHAINFM238Mus musculusMutation(s): 0 
Find proteins for P04213 (Mus musculus)
Explore P04213 
Go to UniProtKB:  P04213
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.422α = 90
b = 83.893β = 92.21
c = 122.273γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-08-03
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2018-12-12
    Changes: Advisory, Data collection, Database references, Source and taxonomy, Structure summary