9OHT | pdb_00009oht

CD1c presenting GD3 ganglioside

• PDB DOI: https://doi.org/10.2210/pdb9OHT/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-05-05 Released: 2025-11-19 
• Deposition Author(s): Cao, T.P., Rossjohn, J., Shahine, A.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Sideways lipid presentation by the antigen-presenting molecule CD1c.

Cao, T.P., Liao, G.R., Cheng, T.Y., Chen, Y., Ciacchi, L., Fulford, T.S., Farquhar, R., Kollmorgen, J., Mayfield, J.A., Uldrich, A.P., Ng, E.Z.Q., Ogg, G.S., Godfrey, D.I., Gherardin, N.A., Chen, Y.L., Moody, D.B., Shahine, A., Rossjohn, J.

(2025) Nat Commun 17: 998-998

• PubMed: 41476042 
• DOI: https://doi.org/10.1038/s41467-025-67732-2
• Primary Citation Related Structures: 
  9OHT, 9OHU, 9OHV, 9OHW, 9OHX, 9OHY, 9OHZ, 9OI0


• PubMed Abstract: 
  

  For the MHC, MR1 and CD1 systems, antigen recognition involves contact of the membrane distal surfaces of both the αβ T cell receptor (TCR) and the antigen-presenting molecule. Whether other antigen display mechanisms by antigen-presenting molecules operate remains unknown. Here, we report mass spectrometry analyses of endogenous lipids captured by CD1c when bound to an autoreactive αβ TCR. CD1c binds twenty-six lipid species with bulky headgroups that cannot fit within the tight TCR-CD1c interface. We determined the crystal structures of CD1c presenting several gangliosides, revealing a general mechanism whereby two lipids, rather than one, are bound in the CD1c cleft. Bulky lipids are oriented sideways so that their polar headgroups protrude laterally through a side portal of the CD1c molecule - an evolutionarily conserved structural feature. The sideways-presented ganglioside headgroups do not hinder TCR binding and so represent a mechanism that allows autoreactive TCR recognition of CD1c. In addition, ex vivo studies showed that the sideways-presented gangliosides can also represent TCR recognition determinants. These findings reveal that CD1c simultaneously presents two lipid antigens from the top and side of its cleft, a general mechanism that differs markedly from other antigen-presenting molecules.

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Organizational Affiliation: 
• Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity at the University of Melbourne, Melbourne, Parkville, VIC, Australia.
Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, UK.
MRC Translational Immune Discovery Unit, Weatherall Institute for Molecular Medicine, University of Oxford, Headington, Oxford, UK.
Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. [e-mail].
Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia. [e-mail].
Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia. [e-mail].
Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.93 kDa 
• Atom Count: 3,145 
• Modeled Residue Count: 379 
• Deposited Residue Count: 382 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein	A	281	Homo sapiens	Mutation(s): 0  Gene Names: CD1C

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	101	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CB4 (Subject of Investigation/LOI)	H [auth A]	(2S,3R,4E)-3-hydroxy-2-octadecanamidooctadec-4-en-1-yl 5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->8)-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside C70 H125 N3 O29 CSXAHYACQIWDLT-JUFCRVMESA-N
A1CB5	D [auth A]	(2S)-2,3-dihydroxypropyl heptadecanoate C20 H40 O4 SVUQHVRAGMNPLW-IBGZPJMESA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
KZF	E [auth A]	2-(cyclohexylazaniumyl)ethanesulfonate C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
MLA	F [auth A], G [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.220 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.496	α = 90
b = 89.496	β = 90
c = 158.438	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Cao, T.P., Rossjohn, J., Shahine, A.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DE210101031

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release
  
• Version 2.0: 2025-12-17
  Type: Coordinate replacement
  Reason: Chirality error
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2026-01-14
  Changes: Database references
• Version 2.2: 2026-02-11
  Changes: Database references