4ONO

CD1c in complex with PM (phosphomycoketide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.705 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.219 

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.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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin/T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein
A
395Homo sapiensMutation(s): 6 
Gene Names: CD1C, B2M, CD1B
Find proteins for P29017 (Homo sapiens)
Go to Gene View: CD1C
Go to UniProtKB:  P29017
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Find proteins for P29016 (Homo sapiens)
Go to Gene View: CD1B
Go to UniProtKB:  P29016
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMK
Query on PMK

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Download CCD File 
A
(4R,8S,16S,20R)-4,8,12,16,20-pentamethylheptacosyl dihydrogen phosphate
C32 H67 O4 P
WLNOCCJMGSEDAT-GCIGRYLYSA-N
 Ligand Interaction
MLI
Query on MLI

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Download CCD File 
A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.705 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.312α = 90.00
b = 86.978β = 90.00
c = 89.574γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling
HKL-2000data collection
PHENIXrefinement
PDB_EXTRACTdata extraction

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
  • Version 1.2: 2017-07-26
    Type: Advisory, Data collection, Refinement description, Source and taxonomy