8SGM: 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 2.5 Å resolution. Released 24 Apr 2024.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,803
Mol. weight: 96.17 kDa
Ligands: A1AHF, NAG
Released: 24 Apr 2024

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

Secondary structure: helices and β-sheets

8SGM contains 19 α-helices and 73 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, 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
β-strand	95-103	9	1
β-strand	111-118	8	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	140-148	9
α-helix	152-159	8
α-helix	160-165	6
α-helix	166-176	11
α-helix	178-182	5
β-strand	185	1	2
β-strand	188-193	6	3
β-strand	201-211	11	3
β-strand	212	1	2
β-strand	216-222	7	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	253-255	3
β-strand	260-265	6	4
β-strand	273-276	4	4

Chain B: 3 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
α-helix	46	1
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

Chain C: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	9-13	5	9
β-strand	18-23	6	8
β-strand	31-38	8	9
β-strand	45-50	6	9
β-strand	55-56	2	8
β-strand	60-64	5	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-92	9	9
β-strand	106-111	6	9
β-strand	120-125	6	10
β-strand	126	1	11
β-strand	133-138	6	10
β-strand	154-156	3	10
α-helix	157-159	3
β-strand	160-164	5	10
α-helix	165-167	3
β-strand	169-178	10	10
β-strand	199	1	10

Chain D: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	12
β-strand	12-16	5	13
β-strand	21-23	3	14
β-strand	26-27	2	12
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	58-59	2	13
β-strand	66-68	3	14
β-strand	75	1	12
β-strand	78-80	3	14
β-strand	89-96	8	13
β-strand	103-105	3	13
β-strand	109-114	6	13
α-helix	117-119	3
β-strand	121	1	15
α-helix	122-123	2
β-strand	124-128	5	11
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	11
β-strand	151	1	15
β-strand	155-161	7	16
β-strand	164-166	3	16
β-strand	170-172	3	11
β-strand	177-178	2	11
β-strand	188-197	10	11
α-helix	198-201	4
β-strand	207-214	8	16
β-strand	217	1	17
α-helix	228-229	2
β-strand	231	1	17
β-strand	233-240	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A	protein	274	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Natural killer T cell receptor TRAV26-2	C	protein	207	Homo sapiens
Natural killer T cell receptor TRBV19 beta chain	D	protein	243	Homo sapiens

Sequence of entity 1 (A), FASTA

>8SGM_1 Antigen-presenting glycoprotein CD1d (chains A)
MQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQW
ETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDI
LSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKK
QVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETW
YLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYQ

Sequence of entity 2 (B), FASTA

>8SGM_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>8SGM_3 Natural killer T cell receptor TRAV26-2 (chains C)
MDAKTTQPNSMESNEEEPVHLPCNHSTISGTDYIHWYRQLPSQGPEYVIHGLTSNVNNRM
ASLAIAEDRKSSTLILHRATLRDAAVYYCILRDGWGGTYKYIFGTGTRLKVLANIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>8SGM_4 Natural killer T cell receptor TRBV19 beta chain (chains D)
MDGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGD
IAEGYSVSREKKESFPLTVTSAQKNPTAFYLCATSVGRPYEQYFGPGTRLTVTEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Ligands and cofactors

ID	Name	Formula	Copies
A1AHF	N-[(2S)-3-oxo-1-(beta-L-talopyranosyloxy)octadecan-2-yl]docosanamide	C46 H89 N O8	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (GOL, SO4) 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.
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

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