4ONH

Crystal Structure of DN6 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 U S A 111: E4648-E4657

  • DOI: 10.1073/pnas.1408549111
  • Primary Citation of Related Structures:  
    4ONO, 4ONH

  • 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 Committee on Immunology, University of Chicago, Chicago, IL 60637; ejadams@uchicago.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor alphaB243Homo sapiensMutation(s): 0 
Gene Names: TRAVTRACTRABTRBC2TCRBC2
Find proteins for A0A5B9 (Homo sapiens)
Explore A0A5B9 
Go to UniProtKB:  A0A5B9
NIH Common Fund Data Resources
PHAROS  A0A5B9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor betaA205Homo sapiensMutation(s): 0 
Gene Names: TRACTCRA
Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
NIH Common Fund Data Resources
PHAROS  P01848
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.825α = 90
b = 64.063β = 115.88
c = 69.534γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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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
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary