3VWK: Antigen-presenting glycoprotein CD1d

Ternary crystal structure of the human NKT TCR-CD1d-4'deoxy-alpha-galactosylceramide complex. Determined by X-ray diffraction at 2.94 Å resolution. Released 3 Oct 2012.

Method: X-ray diffraction
Resolution: 2.94 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,108
Mol. weight: 96.63 kDa
Ligands: MG, 4GH, NAG
Released: 3 Oct 2012

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

Secondary structure: helices and β-sheets

3VWK contains 20 α-helices and 75 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
β-strand	24-32	9	1
β-strand	35-40	6	1
α-helix	47	1
β-strand	48-49	2	1
α-helix	60-87	28
β-strand	94-102	9	1
β-strand	112-118	7	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	166-174	9
α-helix	178-181	4
β-strand	185	1	2
β-strand	188-193	6	3
β-strand	203-211	9	3
β-strand	212	1	2
β-strand	217-220	4	4
β-strand	231-232	2	3
β-strand	236-237	2	3
β-strand	243-250	8	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	6-11	6	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: 5 helices, 18 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	62-67	6	8
α-helix	68-70	3
β-strand	72-77	6	8
α-helix	78	1
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	10
β-strand	129	1	11
β-strand	138-144	7	10
β-strand	158-160	3	10
α-helix	161-163	3
β-strand	164-168	5	10
α-helix	169-171	3
β-strand	173-182	10	10
β-strand	203	1	10

Chain D: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	22-25	4	12
β-strand	32-37	6	13
β-strand	44-49	6	13
β-strand	56-57	2	13
β-strand	65-67	3	14
β-strand	71	1	12
β-strand	74	1	12
β-strand	77-79	3	14
α-helix	84-86	3
β-strand	88-97	10	13
β-strand	103-108	5	13
β-strand	112-117	6	13
α-helix	120-122	3
β-strand	124	1	15
β-strand	127-131	5	16
β-strand	132	1	11
α-helix	135-141	7
β-strand	143-153	11	16
β-strand	154	1	15
β-strand	158-164	7	17
β-strand	168	1	17
β-strand	173-175	3	16
α-helix	179	1
β-strand	180-181	2	16
β-strand	191-200	10	16
α-helix	201-204	4
β-strand	210-217	8	17
β-strand	220	1	18
α-helix	231-232	2
β-strand	234	1	18
β-strand	236-243	8	17

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

>3VWK_1 Antigen-presenting glycoprotein CD1d (chains A)
SPGVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFS
DQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQ
GKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKS
ELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNA
DETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWHHHHHH

Sequence of entity 2 (B), FASTA

>3VWK_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>3VWK_3 NKT15 T cell receptor alpha-chain (chains C)
MKNQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSN
GRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>3VWK_4 NKT15 T cell receptor beta-chain (chains D)
MEADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGD
LSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSGLRDRGLYEQYFGPGTRLTVTEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
4GH	N-{(2S,3R)-1-[(4-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}…	C50 H99 N O7	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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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