9RSE: Human CD1d with lipid antigen bound

Human CD1d with lipid antigen bound. Determined by X-ray diffraction at 1.76 Å resolution. Released 15 Jul 2026.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,207
Mol. weight: 92.92 kDa
Ligands: AGH
Released: 15 Jul 2026

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

Secondary structure: helices and β-sheets

9RSE contains 31 α-helices and 60 β-strands across 4 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: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-20	11	1
β-strand	23-32	10	1
β-strand	35-40	6	1
α-helix	47	1
β-strand	48-49	2	1
α-helix	60-88	29
α-helix	90-91	2
α-helix	93	1
β-strand	94-105	12	1
β-strand	109-118	10	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	141-149	9
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	2
α-helix	186-187	2
β-strand	188-194	7	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	236-237	2	3
α-helix	238	1
β-strand	243-252	10	3
α-helix	253-255	3
β-strand	260-264	5	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	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	36-42	7	7
β-strand	45-46	2	7
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-85	7	7
β-strand	92-95	4	7

Chain C: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-20	11	8
β-strand	23-32	10	8
β-strand	35-40	6	8
α-helix	47	1
β-strand	48-49	2	8
α-helix	60-88	29
α-helix	90-91	2
α-helix	93	1
β-strand	94-104	11	8
α-helix	106-108	3
β-strand	110-118	9	8
β-strand	121-127	7	8
β-strand	130-133	4	8
α-helix	140-149	10
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-182	5
β-strand	185	1	9
α-helix	186-187	2
β-strand	188-193	6	10
β-strand	201-211	11	10
β-strand	212	1	9
β-strand	217-222	6	11
β-strand	225-226	2	11
β-strand	231-232	2	10
β-strand	236-237	2	10
β-strand	243-252	10	10
α-helix	253-255	3
β-strand	259-264	6	11
α-helix	266-268	3
β-strand	273-276	4	11

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	12
α-helix	5-6	2
β-strand	7-12	6	13
β-strand	22-31	10	13
β-strand	32	1	12
β-strand	36-42	7	14
β-strand	45-46	2	14
α-helix	47	1
β-strand	51-52	2	13
α-helix	53-55	3
β-strand	56-57	2	13
β-strand	63-71	9	13
β-strand	79-85	7	14
β-strand	92-95	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A, C	protein	296	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9RSE_1 Antigen-presenting glycoprotein CD1d (chains A, C)
MVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQ
QWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGK
DILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSEL
KKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADE
TWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGPGSGGGLNDIFEAQKIEWH

Sequence of entity 2 (B, D), FASTA

>9RSE_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
AGH	N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}h…	C50 H99 N O9	2

Water and common crystallization additives (1PE) are not listed.

Primary citation

Structural features of human and macaque CD1d: Implications for antigen presentation. Burns, D., Look, A., Turner, S. et al. To be published.

Other PDB entries of the same protein (UniProt P15813 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SOS 2.33 Å, Human CD1d presenting sphingomyelin C24:1 in complex with VHH nanobody 1D17
6V7Y 2.4 Å, Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5
4WW2 2.48 Å, Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8,…
3HUJ 2.5 Å, Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant…
4WO4 2.5 Å, The molecular bases of Delta/Alpha beta T cell-mediated antigen recognition.
8SGM 2.5 Å, Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and…
4EN3 2.57 Å, Crystal structure of a human Valpha24(-) NKT TCR in complex with…
4MQ7 2.6 Å, Structure of human CD1d-sulfatide
6V7Z 2.75 Å, Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22
3U0P 2.8 Å, Crystal structure of human CD1d-lysophosphatidylcholine
8SGB 2.8 Å, Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and…
9O4X 2.86 Å, Gamma delta T cell receptor bound to CD1d

Browse structure collections

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