3HUJ: Human CD1d-alpha-Galactosylceramide

Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor. Determined by X-ray diffraction at 2.5 Å resolution. Released 28 Jul 2009.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,690
Mol. weight: 193.82 kDa
Ligands: MG, AGH, NAG
Released: 28 Jul 2009

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

Secondary structure: helices and β-sheets

3HUJ contains 44 α-helices and 152 β-strands across 8 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: 10 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
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
α-helix	105	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	152-159	8
α-helix	160-165	6
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	1	3
β-strand	236-237	2	3
α-helix	238	1
β-strand	243-252	10	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
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-84	7	7
β-strand	91-94	4	7
α-helix	95-96	2

Chain C: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-20	11	8
β-strand	23-32	10	8
β-strand	35-40	6	8
α-helix	47	1
β-strand	48-49	2	8
α-helix	60-87	28
β-strand	94-104	11	8
β-strand	110-118	9	8
β-strand	121-127	7	8
β-strand	130-133	4	8
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	9
α-helix	186-187	2
β-strand	188-193	6	10
β-strand	204-211	8	10
β-strand	212	1	9
β-strand	217-222	6	11
β-strand	225-226	2	11
β-strand	231-232	2	10
β-strand	236-237	2	10
β-strand	243-249	7	10
β-strand	260-264	5	11
β-strand	273-276	4	11

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Chain E: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	15
β-strand	9-13	5	16
β-strand	18-24	7	15
β-strand	31-37	7	16
β-strand	44-50	7	16
β-strand	55-58	4	15
β-strand	62-67	6	15
α-helix	68-70	3
β-strand	72-77	6	15
α-helix	82-84	3
β-strand	86-93	8	16
β-strand	104-106	3	16
β-strand	110-115	6	16
β-strand	124-127	4	17
β-strand	129	1	18
β-strand	139-142	4	17
β-strand	149	1	19
β-strand	158-160	3	17
α-helix	161-163	3
β-strand	164-168	5	17
β-strand	173-182	10	17
β-strand	197	1	19
β-strand	203	1	17

Chain F: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	20
β-strand	10-14	5	21
β-strand	19-21	3	22
β-strand	22-25	4	20
β-strand	31-37	7	21
β-strand	44-49	6	21
β-strand	56-57	2	21
β-strand	66-67	2	22
β-strand	74	1	20
β-strand	77-79	3	22
α-helix	84-86	3
β-strand	88-97	10	21
β-strand	103-108	5	21
β-strand	112-117	6	21
α-helix	120-122	3
β-strand	124	1	23
α-helix	125-126	2
β-strand	127-131	5	24
β-strand	132	1	18
α-helix	133-134	2
α-helix	135-141	7
β-strand	143-153	11	24
β-strand	154	1	23
β-strand	158-164	7	25
β-strand	167-169	3	25
β-strand	173-175	3	24
α-helix	179	1
β-strand	180-181	2	24
β-strand	191-200	10	24
α-helix	201-205	5
β-strand	210-217	8	25
β-strand	220	1	26
α-helix	231-232	2
β-strand	234	1	26
β-strand	236-243	8	25

Chain G: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	27
β-strand	9-13	5	28
β-strand	18-24	7	27
β-strand	31-37	7	28
β-strand	44-50	7	28
β-strand	55-58	4	27
β-strand	62-67	6	27
β-strand	72-77	6	27
α-helix	82-84	3
β-strand	86-93	8	28
β-strand	104-106	3	28
β-strand	110-115	6	28
β-strand	124-128	5	29
β-strand	129-130	2	30
β-strand	138-142	5	29
α-helix	151-153	3
β-strand	158-160	3	29
α-helix	161-163	3
β-strand	164-168	5	29
β-strand	173-182	10	29
β-strand	203	1	29

Chain H: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	31
β-strand	10-14	5	32
β-strand	19-21	3	33
β-strand	22-25	4	31
β-strand	31-37	7	32
β-strand	44-49	6	32
β-strand	56-57	2	32
β-strand	66-67	2	33
β-strand	71	1	31
β-strand	74	1	31
β-strand	77-79	3	33
α-helix	84-86	3
β-strand	88-97	10	32
β-strand	103-108	5	32
β-strand	112-117	6	32
α-helix	120-122	3
β-strand	124	1	34
α-helix	125-126	2
β-strand	127-132	6	30
α-helix	133-134	2
α-helix	135-138	4
β-strand	143-153	11	30
β-strand	154	1	34
β-strand	158-164	7	35
β-strand	167-169	3	35
β-strand	173-175	3	30
α-helix	179	1
β-strand	180-181	2	30
β-strand	191-200	10	30
α-helix	201-205	5
β-strand	210-217	8	35
β-strand	220	1	36
α-helix	231-232	2
β-strand	234	1	36
β-strand	236-243	8	35

Molecules and chains

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

Sequence of entity 1 (A, C), FASTA

>3HUJ_1 T-cell surface glycoprotein CD1d (chains A, C)
SPGVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFS
DQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQ
GKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKS
ELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNA
DETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWHHHHHH

Sequence of entity 2 (B, D), FASTA

>3HUJ_2 Beta-2-microglobulin (chains B, D)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, G), FASTA

>3HUJ_3 NKT15 T cell receptor alpha-chain (chains E, G)
MKNQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSN
GRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>3HUJ_4 NKT15 T cell receptor beta-chain (chains F, H)
MEADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGD
LSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSGLRDRGLYEQYFGPGTRLTVTEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
AGH	N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}h…	C50 H99 N O9	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors. Pellicci, D.G., Patel, O., Kjer-Nielsen, L. et al. Immunity (2009) 31:47-59. DOI 10.1016/j.immuni.2009.04.018 · 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,…
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…
9O4X 2.86 Å, Gamma delta T cell receptor bound to CD1d

Browse structure collections

About this viewer

MolViewer shows 3HUJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.