9OI0: CD1b presenting ganglioside GD3

Crystal structure of CD1b presenting ganglioside GD3. Determined by X-ray diffraction at 1.84 Å resolution. Released 19 Nov 2025.

Method: X-ray diffraction
Resolution: 1.84 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,590
Mol. weight: 46.88 kDa
Ligands: CUY, A1CDL
Released: 19 Nov 2025

Explore 9OI0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OI0 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	9-20	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	60-84	25
α-helix	91	1
β-strand	94-104	11	1
α-helix	105	1
β-strand	110-118	9	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	154-160	7
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	2
β-strand	188-195	8	3
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	236-238	3	3
β-strand	242-252	11	3
α-helix	253-255	3
β-strand	259-264	6	4
α-helix	266-268	3
β-strand	273-276	4	4

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	36-41	6	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	78-83	6	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1b	A	protein	280	Homo sapiens	P29016 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9OI0_1 T-cell surface glycoprotein CD1b (chains A)
FQGPTSFHVIQTSSFTNSTWAQTQGSGWLDDLQIHGWDSDSGTAIFLKPWSKGNFSDKEV
AELEEIFRVYIFGFAREVQDFAGDFQMKYPFEIQGIAGCELHSGGAIVSFLRGALGGLDF
LSVKNASCVPSPEGGSRAQKFCALIIQYQGIMETVRILLYETCPRYLLGVLNAGKADLQR
QVKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNANWTW
YLRATLDVADGEAAGLSCRVKHSSLEGQDIILYWRGSGLN

Sequence of entity 2 (B), FASTA

>9OI0_2 Beta-2-microglobulin (chains B)
PKIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSK
DWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRD

Ligands and cofactors

ID	Name	Formula	Copies
CUY	tetracosyl octadecanoate	C42 H84 O2	1
A1CDL	N-{(2S,3R,4E)-1-[(4-O-beta-D-galactopyranosyl-beta-D-glucopyranosyl)oxy]-3-hydr…	C48 H91 N O13	1

Water and common crystallization additives (EDO, CL, IOD, NA) are not listed.

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 P29016 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WL1 1.38 Å, Crystal Structure of Human CD1b in Complex with PG
8GLG 1.6 Å, Crystal Structure of Human CD1b in Complex with Phosphatidylethanolamine C34:1
5L2J 1.65 Å, Crystal Structure of human CD1b in complex with C36-GMM
5WKE 1.69 Å, Crystal Structure of Human CD1b in Complex with PS
6D64 1.7 Å, Crystal Structure of Human CD1b in Complex with POPC
7MX4 1.73 Å, CD1c with antigen analogue 1
2H26 1.8 Å, human CD1b in complex with endogenous phosphatidylcholine and spacer
8GLH 1.83 Å, Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5
8GLE 1.85 Å, Crystal Structure of Human CD1b in Complex with Lysosulfatide
3T8X 1.9 Å, Crystal structure of human CD1b in complex with synthetic antigenic…
8DV3 1.9 Å, Crystal structure of human CD1b presenting Phosphatidylinositol C34:1
7MXF 2.0 Å, CD1c with antigen analogue 2

Browse structure collections

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