8SOS: Human CD1d presenting sphingomyelin C24:1

Human CD1d presenting sphingomyelin C24:1 in complex with VHH nanobody 1D17. Determined by X-ray diffraction at 2.33 Å resolution. Released 13 Dec 2023.

Method: X-ray diffraction
Resolution: 2.33 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 8,568
Mol. weight: 132.97 kDa
Ligands: NAG, FO4
Released: 13 Dec 2023

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

Secondary structure: helices and β-sheets

8SOS contains 37 α-helices and 83 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: 11 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	60-87	28
α-helix	90-91	2
α-helix	93	1
β-strand	94-104	11	1
β-strand	110-118	9	1
β-strand	121-127	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	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
α-helix	238	1
β-strand	243-252	10	3
β-strand	260-264	5	4
α-helix	266-268	3
β-strand	273-276	4	4

Chains B and F: 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	36-41	6	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	78-83	6	7
β-strand	91-94	4	7

Chain D: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-13	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	32-39	8	10
β-strand	46-51	6	10
α-helix	57-58	2
β-strand	59-60	2	10
α-helix	62-64	3
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-100	9	10
α-helix	107-110	4
β-strand	116-117	2	10
β-strand	121-123	3	10
β-strand	124-126	3	9

Chain E: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	10-20	11	11
β-strand	23-32	10	11
β-strand	35-40	6	11
α-helix	47	1
β-strand	48-49	2	11
α-helix	60-88	29
α-helix	90-91	2
α-helix	93	1
β-strand	94-105	12	11
β-strand	109-118	10	11
β-strand	121-127	7	11
β-strand	130-133	4	11
α-helix	134	1
α-helix	139-148	10
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	12
β-strand	188-193	6	13
β-strand	204-211	8	13
β-strand	212	1	12
β-strand	217-219	3	14
β-strand	231-232	2	13
β-strand	236-237	2	13
α-helix	238	1
β-strand	243-248	6	13
β-strand	260-264	5	14
α-helix	266-268	3
β-strand	273-276	4	14

Chain G: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	11-13	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	32-39	8	20
β-strand	46-51	6	20
α-helix	57-58	2
β-strand	59-60	2	20
α-helix	62-64	3
β-strand	68-73	6	18
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-100	9	20
α-helix	107-109	3
β-strand	116-117	2	20
β-strand	121-123	3	20
β-strand	124-126	3	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A, E	protein	347	Homo sapiens	P05412 (AlphaFold model), P15813 (AlphaFold model)
Beta-2-microglobulin	B, F	protein	100	Homo sapiens	P61769 (AlphaFold model)
Nanobody VHH ID17	D, G	protein	127	Lama glama

Sequence of entity 1 (A, E), FASTA

>8SOS_1 Antigen-presenting glycoprotein CD1d (chains A, E)
MQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQW
ETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDI
LSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKK
QVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETW
YLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGSLVPRGSGSRIARLEEKVKTLKAQN
SELASTANMLREQVAQLKQKVMNHGSGLNDIFEAQKIEWHEHHHHHH

Sequence of entity 2 (B, F), FASTA

>8SOS_2 Beta-2-microglobulin (chains B, F)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D, G), FASTA

>8SOS_3 Nanobody VHH ID17 (chains D, G)
QVQLVESGGGLVQAGGSLRLSCAASGSSFSSYTMTWFRQAPGKEREIVAGIRWSGESPYY
ADSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAARLVPPGIPIERTLESMRYWGKG
TLVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
FO4	sphingomyelin	C47 H94 N2 O6 P	2

Primary citation

Enhanced CD1d phosphatidylserine presentation using a single-domain antibody promotes immunomodulatory CD1d-TIM-3 interactions. Lameris, R., Shahine, A., Veth, M. et al. J Immunother Cancer (2023) 11. DOI 10.1136/jitc-2023-007631 · PubMed

Other PDB entries of the same protein (UniProt P05412 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Y3V 1.5 Å, 14-3-3 Sigma in complex with phosphorylated c-Jun peptide
5T01 1.89 Å, Human c-Jun DNA binding domain homodimer in complex with methylated DNA
5FV8 1.99 Å, Structure of cJun-FosW coiled coil complex.
1JNM 2.2 Å, Crystal Structure of the Jun/CRE Complex
1A02 2.7 Å, Structure of the DNA binding domains of nfat, fos and jun bound to DNA
1T2K 3.0 Å, Structure Of The DNA Binding Domains Of IRF3, ATF-2 and Jun Bound To DNA
1FOS 3.05 Å, Two human C-fos:c-jun:dna complexes
1S9K 3.1 Å, Crystal Structure of Human NFAT1 and Fos-Jun on the IL-2 ARRE1 Site
1JUN NMR study of C-jun homodimer

Browse structure collections

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