9OHZ: CD1a presenting ganglioside GD3

Crystal structure of CD1a presenting ganglioside GD3. Determined by X-ray diffraction at 2.14 Å resolution. Released 19 Nov 2025.

Method: X-ray diffraction
Resolution: 2.14 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,208
Mol. weight: 46.08 kDa
Ligands: A1CB9, NAG
Released: 19 Nov 2025

Explore 9OHZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OHZ contains 13 α-helices and 30 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
β-strand	24-32	9	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	52-55	4
α-helix	60-88	29
β-strand	94-102	9	1
β-strand	112-118	7	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	135-137	3
α-helix	138-148	11
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-181	16
β-strand	185	1	2
β-strand	188-193	6	3
α-helix	197-198	2
β-strand	201-211	11	3
β-strand	212	1	2
β-strand	217-222	6	4
β-strand	225-226	2	4
β-strand	231-232	2	3
β-strand	236-237	2	3
β-strand	243-252	10	3
α-helix	253-255	3
β-strand	259-264	6	4
α-helix	266-268	3
β-strand	273-276	4	4
α-helix	279-281	3

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-84	7	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1a	A	protein	285	Homo sapiens	P06126 (AlphaFold model)
Beta-2-microglobulin	B	protein	106	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9OHZ_1 T-cell surface glycoprotein CD1a (chains A)
ATGLKEPLSFHVTWIASFYNHSWKQNLVSGWLSDLQTHTWDSNSSTIVFLWPWSRGNFSN
EEWKELETLFRIRTIRSFEGIRRYAHELQFEYPFEIQVTGGCELHSGKVSGSFLQLAYQG
SDFVSFQNNSWLPYPVAGNMAKHFCKVLNQNQHENDITHNLLSDTCPRFILGLLDAGKAH
LQRQVKPEAWLSHGPSPGPGHLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQRGDILPSAD
GTWYLRATLEVAAGEAADLSCRVKHSSLEGQDIVLYWEGSLVPRG

Sequence of entity 2 (B), FASTA

>9OHZ_2 Beta-2-microglobulin (chains B)
AIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGSLVPR

Ligands and cofactors

ID	Name	Formula	Copies
A1CB9	N-{(2S,3R)-1-[(4-O-beta-D-galactopyranosyl-beta-D-glucopyranosyl)oxy]-3-hydroxy…	C54 H105 N O13	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Sideways lipid presentation by the antigen-presenting molecule CD1c. Cao, T.P., Liao, G.R., Cheng, T.Y. et al. Nat Commun (2025) 17:998-998. DOI 10.1038/s41467-025-67732-2 · PubMed

Other PDB entries of the same protein (UniProt P06126 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5J1A 1.86 Å, Antigen presenting molecule
4X6F 1.91 Å, CD1a binary complex with sphingomyelin
7SH4 2.0 Å, CD1a-phosphatidylglycerol binary structure
7KP1 2.02 Å, CD1a-42:2 SM binary complex
4X6E 2.1 Å, CD1a binary complex with lysophosphatidylcholine
1ONQ 2.15 Å, Crystal Structure of CD1a in Complex with a Sulfatide
6NUX 2.2 Å, CD1a-lipid binary complex
7KOZ 2.25 Å, CD1a-36:2 SM binary complex
7KP0 2.4 Å, CD1a-42:1 SM binary complex
7RYN 2.7 Å, CD1a-sulfatide-gdTCR complex
1XZ0 2.8 Å, Crystal structure of CD1a in complex with a synthetic mycobactin lipopeptide
4X6C 2.8 Å, CD1a ternary complex with lysophosphatidylcholine and BK6 TCR

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