6CUG

Crystal structure of BC8B TCR-CD1b-PC complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A T-cell receptor escape channel allows broad T-cell response to CD1b and membrane phospholipids.

Shahine, A.Reinink, P.Reijneveld, J.F.Gras, S.Holzheimer, M.Cheng, T.Y.Minnaard, A.J.Altman, J.D.Lenz, S.Prandi, J.Kubler-Kielb, J.Moody, D.B.Rossjohn, J.Van Rhijn, I.

(2019) Nat Commun 10: 56-56

  • DOI: 10.1038/s41467-018-07898-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CD1 proteins are expressed on dendritic cells, where they display lipid antigens to T-cell receptors (TCRs). Here we describe T-cell autoreactivity towards ubiquitous human membrane phospholipids presented by CD1b. These T-cells discriminate between ...

    CD1 proteins are expressed on dendritic cells, where they display lipid antigens to T-cell receptors (TCRs). Here we describe T-cell autoreactivity towards ubiquitous human membrane phospholipids presented by CD1b. These T-cells discriminate between two major types of lipids, sphingolipids and phospholipids, but were broadly cross-reactive towards diverse phospholipids including phosphatidylcholine, phosphatidylinositol and phosphatidylethanolamine. The crystal structure of a representative TCR bound to CD1b-phosphatidylcholine provides a molecular mechanism for this promiscuous recognition. We observe a lateral escape channel in the TCR, which shunted phospholipid head groups sideways along the CD1b-TCR interface, without contacting the TCR. Instead the TCR recognition site involved the neck region phosphate that is common to all major self-phospholipids but absent in sphingolipids. Whereas prior studies have focused on foreign lipids or rare self-lipids, we define a new molecular mechanism of promiscuous recognition of common self-phospholipids including those that are known targets in human autoimmune disease.


    Organizational Affiliation

    Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea.,Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; baumeist@biochem.mpg.de.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea. sglee@kribb.re.kr.,Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, 02115, USA.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA.,Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, 02115, USA. I.vanRhijn@uu.nl.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands. I.vanRhijn@uu.nl.,Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea. sglee@kribb.re.kr.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.,Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France.,Stratingh Institute for Chemistry, University of Groningen, 9747AG, Groningen, The Netherlands.,Department of Biophysics, Ruhr University Bochum, 44801 Bochum, Germany.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK. Jamie.rossjohn@monash.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1b
A
300Homo sapiensMutation(s): 0 
Gene Names: CD1B
Find proteins for P29016 (Homo sapiens)
Go to Gene View: CD1B
Go to UniProtKB:  P29016
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Homo 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
T-cell receptor alpha variable TRAV9-2 - BC8B TCR
D
207N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor beta variable TRBV6-2 - BC8B TCR
E
245N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CUY
Query on CUY

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Download CCD File 
A
tetracosyl octadecanoate
C42 H84 O2
JKKQRJTZBKHHOI-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
POV
Query on POV

Download SDF File 
Download CCD File 
D
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
POPC
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.300α = 90.00
b = 65.700β = 100.70
c = 101.900γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PHASERphasing
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release