3C60

Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR YAe62

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.267 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crossreactive T Cells spotlight the germline rules for alphabeta T cell-receptor interactions with MHC molecules.

Dai, S., Huseby, E.S., Rubtsova, K., Scott-Browne, J., Crawford, F., Macdonald, W.A., Marrack, P., Kappler, J.W.

(2008) Immunity 28: 324-334

  • DOI: 10.1016/j.immuni.2008.01.008
  • Primary Citation of Related Structures:  
    3C5Z, 3C60, 3C6L

  • PubMed Abstract: 

    • To test whether highly crossreactive alphabeta T cell receptors (TCRs) produced during limited negative selection best illustrate evolutionarily conserved interactions between TCR and major histocompatibility complex (MHC) molecules, we solved the st ...

    To test whether highly crossreactive alphabeta T cell receptors (TCRs) produced during limited negative selection best illustrate evolutionarily conserved interactions between TCR and major histocompatibility complex (MHC) molecules, we solved the structures of three TCRs bound to the same MHC II peptide (IAb-3K). The TCRs had similar affinities for IAb-3K but varied from noncrossreactive to extremely crossreactive with other peptides and MHCs. Crossreactivity correlated with a shrinking, increasingly hydrophobic TCR-ligand interface, involving fewer TCR amino acids. A few CDR1 and CDR2 amino acids dominated the most crossreactive TCR interface with MHC, including Vbeta8 48Y and 54E and Valpha4 29Y, arranged to impose the familiar diagonal orientation of TCR on MHC. These interactions contribute to MHC binding by other TCRs using related V regions, but not usually so dominantly. These data show that crossreactive TCRs can spotlight the evolutionarily conserved features of TCR-MHC interactions and that these interactions impose the diagonal docking of TCRs on MHC.

    Organizational Affiliation: 

    Howard Hughes Medical Institute and National Jewish Medical and Research Center, Denver, CO 80206, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TCR YAe62 alpha chainA, E199Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TCR YAe62 beta chainB, F236Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, A-B alpha chainC, G182Mus musculusMutation(s): 0 
Gene Names: H2-Aa
Find proteins for P14434 (Mus musculus)
Explore P14434 
Go to UniProtKB:  P14434
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain)D, H217Mus musculusMutation(s): 1 
Gene Names: H2-Ab1, H2-iabeta
Find proteins for P14483 (Mus musculus)
Explore P14483 
Go to UniProtKB:  P14483
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.267 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.058α = 90
b = 126.168β = 90
c = 277.184γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-02-01 
  • Released Date: 2008-04-29 
    • Deposition Author(s): Dai, S.

Revision History 

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2020-02-05
    Changes: Database references, Derived calculations