3U0P: Human CD1d-lysophosphatidylcholine

Crystal structure of human CD1d-lysophosphatidylcholine. Determined by X-ray diffraction at 2.8 Å resolution. Released 25 Apr 2012.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,971
Mol. weight: 137.96 kDa
Ligands: HEX, LSC, NBU, UND
Released: 25 Apr 2012

Explore 3U0P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3U0P contains 34 α-helices and 88 β-strands across 6 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
β-strand	24-32	9	1
β-strand	35-40	6	1
β-strand	47-49	3	1
α-helix	60-87	28
α-helix	90-91	2
α-helix	93	1
β-strand	94-104	11	1
β-strand	110-118	9	1
β-strand	121-126	6	1
β-strand	131-133	3	1
α-helix	140-150	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
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	253-256	4
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	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
α-helix	46	1
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-84	7	7
β-strand	91-94	4	7

Chain C: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	8
β-strand	24-32	9	8
β-strand	35-40	6	8
β-strand	48-49	2	8
α-helix	61-87	27
α-helix	90-91	2
α-helix	93	1
β-strand	94-103	10	8
α-helix	109-110	2
β-strand	111-118	8	8
β-strand	121-127	7	8
β-strand	130-133	4	8
α-helix	140-148	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	9
β-strand	188-193	6	10
β-strand	201-211	11	10
β-strand	212	1	9
β-strand	216-222	7	11
β-strand	225-226	2	11
β-strand	228	1	12
β-strand	230	1	12
β-strand	231-232	2	10
β-strand	236-237	2	10
α-helix	238	1
β-strand	243-252	10	10
α-helix	253-256	4
β-strand	259-265	7	11
β-strand	273-276	4	11
α-helix	277	1

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	13
α-helix	4-5	2
β-strand	6-11	6	14
β-strand	21-30	10	14
β-strand	31	1	13
β-strand	36-41	6	15
β-strand	44-45	2	15
β-strand	50-51	2	14
α-helix	52-54	3
β-strand	55-56	2	14
β-strand	62-70	9	14
β-strand	78-83	6	15
β-strand	91-94	4	15

Chain E: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	16
β-strand	24-32	9	16
β-strand	35-40	6	16
β-strand	48-49	2	16
α-helix	63-88	26
α-helix	90-91	2
α-helix	93	1
β-strand	94-103	10	16
β-strand	111-118	8	16
β-strand	121-127	7	16
β-strand	130-133	4	16
α-helix	139-150	12
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-175	10
α-helix	178-182	5
β-strand	185	1	17
β-strand	188	1	18
β-strand	208-211	4	18
β-strand	212	1	17
β-strand	217	1	19
β-strand	236-237	2	18
β-strand	243-245	3	18
β-strand	264	1	19

Chain F: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	20
β-strand	6-11	6	21
β-strand	23-30	8	21
β-strand	31	1	20
β-strand	38	1	22
β-strand	51	1	21
α-helix	52-54	3
β-strand	55-56	2	21
β-strand	62-66	5	21
β-strand	81	1	22
β-strand	92	1	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A, C, E	protein	284	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B, D, F	protein	102	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>3U0P_1 Antigen-presenting glycoprotein CD1d (chains A, C, E)
ADPVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSQDSDTVRSLKPWSQGTFS
DQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGQASNNFFHVAFQ
GKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLQGTCPQFVSGLLESGKS
ELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNA
DETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWHHHHHH

Sequence of entity 2 (B, D, F), FASTA

>3U0P_2 Beta-2-microglobulin (chains B, D, F)
ADPIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFS
KDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
HEX	Hexane	C6 H14	1
LSC	(4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos…	C26 H53 N O7 P	2
NBU	N-butane	C4 H10	1
UND	Undecane	C11 H24	1

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor. Lopez-Sagaseta, J., Sibener, L.V., Kung, J.E. et al. EMBO J (2012) 31:2047-2059. DOI 10.1038/emboj.2012.54 · PubMed

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

9RSE 1.76 Å, Human CD1d with lipid antigen bound
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
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

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