3VWJ: Antigen-presenting glycoprotein CD1d

Ternary crystal structure of the human NKT TCR-CD1d-C20:2 complex. Determined by X-ray diffraction at 3.09 Å resolution. Released 3 Oct 2012.

Method: X-ray diffraction
Resolution: 3.09 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,969
Mol. weight: 96.57 kDa
Ligands: NAG, DB3, MG
Released: 3 Oct 2012

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

Secondary structure: helices and β-sheets

3VWJ contains 15 α-helices and 76 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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	10-20	11	1
β-strand	23-32	10	1
β-strand	35-40	6	1
β-strand	48-49	2	1
α-helix	60-87	28
α-helix	90-91	2
α-helix	93	1
β-strand	94-99	6	1
β-strand	102	1	1
β-strand	112	1	1
β-strand	115-118	4	1
β-strand	121-125	5	1
β-strand	132-133	2	1
α-helix	141-148	8
α-helix	152-159	8
α-helix	160-165	6
α-helix	166-175	10
β-strand	185	1	2
β-strand	188-193	6	3
β-strand	203-211	9	3
β-strand	212	1	2
β-strand	217-219	3	4
β-strand	231-238	8	3
β-strand	242-250	9	3
β-strand	261	1	5
β-strand	262-264	3	4
β-strand	275	1	5

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	7-11	5	6
β-strand	21-30	10	6
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: 1 helix, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	8
β-strand	9-13	5	9
β-strand	18-23	6	10
β-strand	24	1	8
β-strand	31-37	7	9
β-strand	44-50	7	9
β-strand	55-57	3	10
β-strand	62-65	4	10
β-strand	67	1	10
β-strand	72-77	6	10
α-helix	82-84	3
β-strand	86-93	8	9
β-strand	104-106	3	9
β-strand	110-115	6	9
β-strand	124-128	5	11
β-strand	129	1	12
β-strand	138-142	5	11
β-strand	159-160	2	13
β-strand	164-168	5	11
β-strand	173-178	6	11
β-strand	180-181	2	13
β-strand	203	1	11

Chain D: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-14	5	15
β-strand	19-21	3	16
β-strand	22-25	4	14
β-strand	31-37	7	15
β-strand	43-51	9	15
β-strand	54-57	4	15
β-strand	65-67	3	16
β-strand	74	1	14
β-strand	77-79	3	16
β-strand	89-97	9	15
β-strand	103-108	5	15
α-helix	109	1
β-strand	112-117	6	15
α-helix	120-122	3
β-strand	127-131	5	17
β-strand	132	1	12
α-helix	135-140	6
β-strand	143-153	11	17
β-strand	158-164	7	18
β-strand	168-169	2	18
β-strand	173-175	3	17
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	237-238	2	18
β-strand	241-243	3	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A	protein	284	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
NKT15 T cell receptor alpha-chain	C	protein	209	Homo sapiens
NKT15 T cell receptor beta-chain	D	protein	246	Homo sapiens

Sequence of entity 1 (A), FASTA

>3VWJ_1 Antigen-presenting glycoprotein CD1d (chains A)
SPGVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFS
DQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQ
GKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKS
ELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNA
DETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWHHHHHH

Sequence of entity 2 (B), FASTA

>3VWJ_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>3VWJ_3 NKT15 T cell receptor alpha-chain (chains C)
MKNQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSN
GRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>3VWJ_4 NKT15 T cell receptor beta-chain (chains D)
MEADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGD
LSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSGLRDRGLYEQYFGPGTRLTVTEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
DB3	(11Z,14E)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-…	C44 H83 N O9	1
MG	Magnesium ion	Mg	1

Primary citation

Human and mouse type I natural killer T cell antigen receptors exhibit different fine specificities for CD1d-antigen complex. Wun, K.S., Ross, F., Patel, O. et al. J Biol Chem (2012) 287:39139-39148. DOI 10.1074/jbc.M112.412320 · 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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