4ONH

Crystal Structure of DN6 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.008 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by alpha beta T cells.

Roy, S.Ly, D.Li, N.S.Altman, J.D.Piccirilli, J.A.Moody, D.B.Adams, E.J.

(2014) Proc.Natl.Acad.Sci.USA 111: E4648-E4657

  • DOI: 10.1073/pnas.1408549111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CD1c is a member of the group 1 CD1 family of proteins that are specialized for lipid antigen presentation. Despite high cell surface expression of CD1c on key antigen-presenting cells and the discovery of its mycobacterial lipid antigen presentation ...

    CD1c is a member of the group 1 CD1 family of proteins that are specialized for lipid antigen presentation. Despite high cell surface expression of CD1c on key antigen-presenting cells and the discovery of its mycobacterial lipid antigen presentation capability, the molecular basis of CD1c recognition by T cells is unknown. Here we present a comprehensive functional and molecular analysis of αβ T-cell receptor (TCR) recognition of CD1c presenting mycobacterial phosphomycoketide antigens. Our structure of CD1c with the mycobacterial phosphomycoketide (PM) shows similarities to that of CD1c-mannosyl-β1-phosphomycoketide in that the A' pocket accommodates the mycoketide alkyl chain; however, the phosphate head-group of PM is shifted ∼6 Å in relation to that of mannosyl-β1-PM. We also demonstrate a bona fide interaction between six human TCRs and CD1c-mycoketide complexes, measuring high to moderate affinities. The crystal structure of the DN6 TCR and mutagenic studies reveal a requirement of five complementarity determining region (CDR) loops for CD1c recognition. Furthermore, mutagenesis of CD1c reveals residues in both the α1 and α2 helices involved in TCR recognition, yet not entirely overlapping among the examined TCRs. Unlike patterns for MHC I, no archetypical binding footprint is predicted to be shared by CD1c-reactive TCRs, even when recognizing the same or similar antigens.


    Organizational Affiliation

    Departments of Biochemistry and Molecular Biology and Chemistry and.,Departments of Biochemistry and Molecular Biology and.,Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115; and.,Departments of Biochemistry and Molecular Biology and Committee on Immunology, University of Chicago, Chicago, IL 60637; ejadams@uchicago.edu.,Emory Vaccine Center at Yerkes, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30329.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor alpha
B
243Homo sapiensMutation(s): 0 
Gene Names: TRBC2 (TCRBC2)
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor beta
A
205Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.008 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.825α = 90.00
b = 64.063β = 115.88
c = 69.534γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-01-28 
  • Released Date: 2014-10-08 
  • Deposition Author(s): Roy, S., Adams, E.J.

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2015-02-18
    Type: Database references