9OHV | pdb_00009ohv

CD1c presenting dual lipids MPM and GD3 ganglioside

• PDB DOI: https://doi.org/10.2210/pdb9OHV/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: 2.12 Å
• R-Value Free: 
  0.260 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

CD1c presenting dual lipids MPM and GD3 ganglioside

Cao, T.P., Rossjohn, J., Shahine, A.

To be published.

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: 45.76 kDa 
• Atom Count: 3,205 
• Modeled Residue Count: 374 
• Deposited Residue Count: 378 
• 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	280	Homo sapiens	Mutation(s): 0  Gene Names: CD1C
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	98	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)	D [auth A]	(2R,3R,4E)-3-hydroxy-2-octadecanamidooctadec-4-en-1-yl 5-acetamido-3,5-dideoxy-L-glycero-beta-L-altro-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-ZNUNQQKYSA-N
MK0 (Subject of Investigation/LOI)	E [auth A]	1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose C38 H77 O9 P BWDAWKXFHWFXEQ-RIEBCBCMSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
KZF	G [auth A]	2-(cyclohexylazaniumyl)ethanesulfonate C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.260 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.915	α = 90
b = 84.941	β = 90
c = 93.219	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

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