8SGB: CD1d-lipid

Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and TCR Beta-Chain. Determined by X-ray diffraction at 2.8 Å resolution. Released 24 Apr 2024.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,439
Mol. weight: 104.08 kDa
Ligands: NAG, FO4
Released: 24 Apr 2024

Explore 8SGB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SGB contains 17 α-helices and 72 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: 7 helices, 17 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	48-49	2	1
α-helix	60-87	28
β-strand	94-103	10	1
β-strand	111-118	8	1
β-strand	121-126	6	1
β-strand	131-133	3	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	2
β-strand	201-211	11	2
β-strand	217-222	6	3
β-strand	225-226	2	3
β-strand	230-232	3	2
β-strand	236-237	2	2
β-strand	243-252	10	2
α-helix	254-256	3
β-strand	260-264	5	3
β-strand	273-276	4	3

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	4
α-helix	4-5	2
β-strand	6-11	6	5
β-strand	21-30	10	5
β-strand	31	1	4
β-strand	36-41	6	6
β-strand	44-45	2	6
α-helix	46	1
β-strand	50-51	2	5
α-helix	52-54	3
β-strand	55-56	2	5
β-strand	62-70	9	5
β-strand	78-83	6	6
β-strand	91-94	4	6

Chain C: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	9-13	5	8
β-strand	16-23	8	7
β-strand	31-38	8	8
β-strand	45-50	6	8
β-strand	55-56	2	7
β-strand	60-64	5	7
β-strand	70-78	9	7
α-helix	80-82	3
β-strand	85-92	8	8
β-strand	106-111	6	8
β-strand	120-125	6	9
β-strand	126	1	10
β-strand	133-138	6	9
α-helix	147-149	3
β-strand	155-156	2	9
β-strand	160-163	4	9
β-strand	170-177	8	9
α-helix	191-193	3
β-strand	199	1	9

Chain D: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	11
β-strand	12-13	2	12
β-strand	16	1	13
β-strand	19	1	13
β-strand	22-23	2	14
β-strand	26-27	2	11
β-strand	33-39	7	12
β-strand	46-53	8	12
β-strand	56-59	4	12
β-strand	67-68	2	14
β-strand	75	1	11
β-strand	78-79	2	14
β-strand	89-96	8	12
β-strand	103-105	3	12
β-strand	109-111	3	12
β-strand	114	1	13
β-strand	121	1	15
β-strand	124-128	5	10
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	10
β-strand	151	1	15
β-strand	155-161	7	16
β-strand	164-166	3	16
β-strand	170-172	3	10
β-strand	177-178	2	10
β-strand	188-197	10	10
α-helix	198-201	4
β-strand	207-214	8	16
α-helix	228-229	2
β-strand	234-240	7	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A	protein	347	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Natural Killer T cell receptor TRAV26A-2 alpha chain	C	protein	207	Homo sapiens
Natural Killer T cell receptor TRBV19 beta chain	D	protein	243	Homo sapiens

Sequence of entity 1 (A), FASTA

>8SGB_1 Antigen-presenting glycoprotein CD1d (chains A)
MQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQW
ETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDI
LSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKK
QVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETW
YLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGSLVPRGSGSRIARLEEKVKTLKAQN
SELASTANMLREQVAQLKQKVMNHGSGLNDIFEAQKIEWHEHHHHHH

Sequence of entity 2 (B), FASTA

>8SGB_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>8SGB_3 Natural Killer T cell receptor TRAV26A-2 alpha chain (chains C)
MDAKTTQPNSMESNEEEPVHLPCNHSTISGTDYIHWYRQLPSQGPEYVIHGLTSNVNNRM
ASLAIAEDRKSSTLILHRATLRDAAVYYCILRDGWGGTYKYIFGTGTRLKVLANIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>8SGB_4 Natural Killer T cell receptor TRBV19 beta chain (chains D)
MDGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGD
IAEGYSVSREKKESFPLTVTSAQKNPTAFYLCATSVGRPYEQYFGPGTRLTVTEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
FO4	sphingomyelin	C47 H94 N2 O6 P	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Semi-invariant human type II Natural Killer T cells recognise CD1d independently of bound lipids. Chan Yew Poa, K.T.O., Le Nours, J., Rossjohn, J. 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:

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
9O4X 2.86 Å, Gamma delta T cell receptor bound to CD1d

Browse structure collections

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