6C09

Ternary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

T cell autoreactivity directed toward CD1c itself rather than toward carried self lipids.

Wun, K.S.Reijneveld, J.F.Cheng, T.Y.Ladell, K.Uldrich, A.P.Le Nours, J.Miners, K.L.McLaren, J.E.Grant, E.J.Haigh, O.L.Watkins, T.S.Suliman, S.Iwany, S.Jimenez, J.Calderon, R.Tamara, K.L.Leon, S.R.Murray, M.B.Mayfield, J.A.Altman, J.D.Purcell, A.W.Miles, J.J.Godfrey, D.I.Gras, S.Price, D.A.Van Rhijn, I.Moody, D.B.Rossjohn, J.

(2018) Nat. Immunol. 19: 397-406

  • DOI: 10.1038/s41590-018-0065-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The hallmark function of αβ T cell antigen receptors (TCRs) involves the highly specific co-recognition of a major histocompatibility complex molecule and its carried peptide. However, the molecular basis of the interactions of TCRs with the lipid an ...

    The hallmark function of αβ T cell antigen receptors (TCRs) involves the highly specific co-recognition of a major histocompatibility complex molecule and its carried peptide. However, the molecular basis of the interactions of TCRs with the lipid antigen-presenting molecule CD1c is unknown. We identified frequent staining of human T cells with CD1c tetramers across numerous subjects. Whereas TCRs typically show high specificity for antigen, both tetramer binding and autoreactivity occurred with CD1c in complex with numerous, chemically diverse self lipids. Such extreme polyspecificity was attributable to binding of the TCR over the closed surface of CD1c, with the TCR covering the portal where lipids normally protrude. The TCR essentially failed to contact lipids because they were fully seated within CD1c. These data demonstrate the sequestration of lipids within CD1c as a mechanism of autoreactivity and point to small lipid size as a determinant of autoreactive T cell responses.


    Related Citations: 
    • To be added later
      Wun, K.S.,Rossjohn, J.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1c
A
287Homo sapiensMutation(s): 0 
Gene Names: CD1C
Find proteins for P29017 (Homo sapiens)
Go to Gene View: CD1C
Go to UniProtKB:  P29017
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
108Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
3C8 T cell receptor alpha-chain
C
205N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
3C8 T cell receptor beta-chain
D
247N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

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Download CCD File 
A
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 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
EKG
Query on EKG

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl hexadecanoate
C19 H38 O4
QHZLMUACJMDIAE-GOSISDBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 173.170α = 90.00
b = 173.170β = 90.00
c = 82.470γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)Australia--
Australian Research CouncilAustralia--

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2018-04-04
    Type: Data collection, Database references