3C6L

Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR 2W20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.268 

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:  

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TCR 2W20 alpha chain
A, E
185N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TCR 2W20 beta chain
B, F
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
H-2 class II histocompatibility antigen, A-B alpha chain
C, G
182Mus musculusMutation(s): 0 
Gene Names: H2-Aa
Find proteins for P14434 (Mus musculus)
Go to UniProtKB:  P14434
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
3K peptide, Linker,and H-2 class II histocompatibility antigen (A beta chain)
D, H
217Mus musculusMutation(s): 1 
Gene Names: H2-Ab1 (H2-iabeta)
Find proteins for P14483 (Mus musculus)
Go to UniProtKB:  P14483
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.268 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.540α = 90.00
b = 113.930β = 90.00
c = 386.260γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PHASESphasing
PHASERphasing
ADSCdata collection
HKL-3000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-02-04 
  • 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
    Type: Version format compliance
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-10-25
    Type: Refinement description