Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 96.71 kDa 
• Atom Count: 6245 
• Residue Count: 803 
• Unique protein chains: 4

6C09

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

• DOI: 10.2210/pdb6C09/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-12-28 Released: 2018-03-21 
• Deposition Author(s): Wun, K.S., Rossjohn, J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

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

• PubMed: 29531339 
• DOI: 10.1038/s41590-018-0065-7
• Primary Citation of Related Structures:  
  6C09, 6C15


• 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 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.

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Related Citations: 

• To be added later
  Wun, K.S., Rossjohn, J.
  () To be published --: --

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Organizational Affiliation: 

Division of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD1c	A	287	Homo sapiens	Mutation(s): 0  Gene Names: CD1C
Find proteins for P29017 (Homo sapiens) Explore P29017  Go to UniProtKB:  P29017
NIH Common Fund Data Resources
PHAROS  P29017 GTEx  ENSG00000158481

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	108	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
3C8 T cell receptor alpha-chain	C	205	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
3C8 T cell receptor beta-chain	D	247	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EKG	A	(2R)-2,3-dihydroxypropyl hexadecanoate C19 H38 O4 QHZLMUACJMDIAE-GOSISDBHSA-N
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
D10	A	DECANE C10 H22 DIOQZVSQGTUSAI-UHFFFAOYSA-N
PEG	C	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	C	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	A, D	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.17	α = 90
b = 173.17	β = 90
c = 82.47	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-12-28 
• Released Date: 2018-03-21 
Deposition Author(s): Wun, K.S., Rossjohn, J.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--
Australian Research Council (ARC)	Australia	--

Revision History 

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2018-03-28
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.2: 2018-04-04
  Changes: Data collection, Database references
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary