2PO6: CD1d-lipid-antigen

Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain. Determined by X-ray diffraction at 3.2 Å resolution. Released 3 Jul 2007.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,298
Mol. weight: 191.08 kDa
Ligands: AGH, NAG
Released: 3 Jul 2007

Explore 2PO6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PO6 contains 43 α-helices and 147 β-strands across 8 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	1
β-strand	20	1	2
β-strand	23	1	2
β-strand	26-32	7	1
β-strand	35-40	6	1
α-helix	47	1
β-strand	48-49	2	1
α-helix	60-88	29
β-strand	96-104	9	1
β-strand	110-118	9	1
β-strand	121-127	7	1
β-strand	130-133	4	1
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	188-193	6	3
β-strand	201-211	11	3
β-strand	217-221	5	4
β-strand	226	1	4
β-strand	231-237	7	3
α-helix	238	1
β-strand	243-252	10	3
α-helix	253-255	3
β-strand	260-264	5	4
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	8-11	4	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

Chain C: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	9-13	5	9
β-strand	18-24	7	8
β-strand	31-37	7	9
β-strand	44-50	7	9
β-strand	55-58	4	8
β-strand	62-65	4	8
β-strand	67	1	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	87-93	7	9
β-strand	104-106	3	9
β-strand	110-115	6	9
β-strand	124-128	5	10
β-strand	129	1	11
α-helix	130-131	2
β-strand	137-142	6	10
β-strand	158-160	3	10
α-helix	161-163	3
β-strand	166-168	3	12
β-strand	173-175	3	12
β-strand	177-182	6	10
β-strand	203	1	10

Chain D: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-21	3	15
β-strand	22-25	4	13
β-strand	31-37	7	14
β-strand	44-51	8	14
β-strand	54-57	4	14
β-strand	66-67	2	15
β-strand	71	1	13
β-strand	74	1	13
β-strand	77-79	3	15
α-helix	84-86	3
β-strand	89-95	7	14
β-strand	106-108	3	14
β-strand	112-117	6	14
α-helix	120-122	3
β-strand	124	1	16
α-helix	125-126	2
β-strand	127-131	5	17
β-strand	132	1	11
α-helix	133-134	2
α-helix	135-141	7
β-strand	143-153	11	17
β-strand	154	1	16
β-strand	158-164	7	18
β-strand	167-169	3	18
β-strand	173-175	3	17
α-helix	179	1
β-strand	180-181	2	17
β-strand	191-200	10	17
α-helix	201-205	5
β-strand	210-217	8	18
β-strand	220	1	19
β-strand	234	1	19
β-strand	236-243	8	18

Chain E: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	10-20	11	20
β-strand	23-32	10	20
β-strand	35-40	6	20
β-strand	47-49	3	20
α-helix	60-87	28
β-strand	94-104	11	20
β-strand	110-118	9	20
β-strand	121-127	7	20
β-strand	130-133	4	20
α-helix	141-148	8
α-helix	156-160	5
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	188-193	6	21
β-strand	201-211	11	21
β-strand	216-219	4	22
β-strand	231-232	2	21
β-strand	236-237	2	21
β-strand	243-252	10	21
α-helix	253-255	3
β-strand	260-265	6	22
β-strand	273-276	4	22

Chain F: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	6-11	6	23
β-strand	21-30	10	23
β-strand	36-41	6	24
β-strand	44-45	2	24
β-strand	50	1	23
β-strand	55-56	2	23
β-strand	62-70	9	23
β-strand	78-84	7	24
β-strand	87-94	8	24
α-helix	95-96	2

Chain G: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	25
β-strand	9-13	5	26
β-strand	18-24	7	25
β-strand	31-37	7	26
β-strand	43-50	8	26
β-strand	55-58	4	25
β-strand	62-67	6	25
β-strand	72-77	6	25
α-helix	82-84	3
β-strand	86-93	8	26
β-strand	104-106	3	26
β-strand	110-115	6	26
α-helix	116	1
β-strand	124-128	5	27
α-helix	129-130	2
β-strand	137-142	6	27
α-helix	150-152	3
β-strand	158-160	3	27
α-helix	161-163	3
β-strand	166-168	3	28
α-helix	169-171	3
β-strand	173-175	3	28
β-strand	177-182	6	27
β-strand	203	1	27

Chain H: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	29
β-strand	10-14	5	30
β-strand	19-21	3	31
β-strand	22-25	4	29
β-strand	31-36	6	30
β-strand	44-51	8	30
β-strand	54-57	4	30
β-strand	66-67	2	31
β-strand	71	1	29
β-strand	74	1	29
β-strand	77-79	3	31
α-helix	84-86	3
β-strand	89-95	7	30
β-strand	106-108	3	30
β-strand	112-117	6	30
α-helix	120-122	3
β-strand	124	1	32
β-strand	127-131	5	33
α-helix	132-134	3
α-helix	135-140	6
β-strand	143-153	11	33
β-strand	154	1	32
β-strand	158-164	7	34
β-strand	167-169	3	34
β-strand	173-175	3	33
α-helix	179	1
β-strand	180-181	2	33
β-strand	191-200	10	33
α-helix	201-204	4
β-strand	210-217	8	34
β-strand	220	1	35
β-strand	234	1	35
β-strand	236-243	8	34
α-helix	244-245	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1d	A, E	protein	278	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B, F	protein	99	Homo sapiens	P61769 (AlphaFold model)
NKT15 alpha-chain	C, G	protein	204	Homo sapiens	P01848 (AlphaFold model)
NKT15 beta-chain	D, H	protein	244	Homo sapiens	P0DTU4 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>2PO6_1 T-cell surface glycoprotein CD1d (chains A, E)
RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWET
LQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILS
FQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQV
KPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYL
RATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWHHHHHH

Sequence of entity 2 (B, F), FASTA

>2PO6_2 Beta-2-microglobulin (chains B, F)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, G), FASTA

>2PO6_3 NKT15 alpha-chain (chains C, G)
NQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSNGR
YTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSP

Sequence of entity 4 (D, H), FASTA

>2PO6_4 NKT15 beta-chain (chains D, H)
ADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGDLS
SESTVSRIRTEHFPLTLESARPSHTSQYLCASSGLRDRGLYEQYFGPGTRLTVTEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

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
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor. Borg, N.A., Wun, K.S., Kjer-Nielsen, L. et al. Nature (2007) 448:44-49. DOI 10.1038/nature05907 · 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
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…

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