6C15

CD1c in complex with phosphatidylcholine

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens

  • Deposited: 2018-01-03 Released: 2018-03-21 
  • Deposition Author(s): Wun, K.S., Rossjohn, J.
  • Funding Organization(s): National Health and Medical Research Council (Australia); Australian Research Council 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.208 

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
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
D12
Query on D12

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Download CCD File 
A
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
6PL
Query on 6PL

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Download CCD File 
A
(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
1-PALMITOYL-2-STEAROYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H85 N O8 P
PZNPLUBHRSSFHT-RRHRGVEJSA-O
 Ligand Interaction
EDO
Query on EDO

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

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Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-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
MES
Query on MES

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.208 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 84.255α = 90.00
b = 84.255β = 90.00
c = 366.833γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
BUSTERrefinement
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
  • Version 1.2: 2018-04-04
    Type: Data collection, Database references