4EN3: Human Valpha24(-) NKT TCR

Crystal structure of a human Valpha24(-) NKT TCR in complex with CD1d/alpha-galactosylceramide. Determined by X-ray diffraction at 2.57 Å resolution. Released 31 Oct 2012.

Method: X-ray diffraction
Resolution: 2.57 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,381
Mol. weight: 100.36 kDa
Ligands: FUC, AGH, NAG
Released: 31 Oct 2012

Explore 4EN3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4EN3 contains 22 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: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	5
β-strand	18-23	6	6
β-strand	30-36	7	5
β-strand	43-49	7	5
β-strand	54-57	4	6
β-strand	60-65	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-91	8	5
β-strand	100-102	3	5
β-strand	106-111	6	5
β-strand	120-124	5	7
β-strand	126	1	8
β-strand	134-138	5	7
β-strand	155-156	2	7
α-helix	160	1
β-strand	161-162	2	9
β-strand	173-177	5	7
α-helix	185-187	3
β-strand	199	1	7

Chain B: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-14	5	11
β-strand	19-21	3	12
β-strand	22-25	4	10
β-strand	31-37	7	11
β-strand	43-49	7	11
β-strand	56-57	2	11
β-strand	65-66	2	12
β-strand	73	1	10
β-strand	76-78	3	12
α-helix	83-85	3
β-strand	87-94	8	11
α-helix	95-96	2
β-strand	106-107	2	11
β-strand	111-116	6	11
α-helix	119-121	3
β-strand	123	1	13
α-helix	124-125	2
β-strand	126-130	5	8
α-helix	131-133	3
α-helix	134-137	4
β-strand	142-152	11	8
β-strand	153	1	13
β-strand	157-163	7	14
β-strand	166-168	3	14
β-strand	172	1	8
β-strand	173-174	2	9
α-helix	178	1
β-strand	179-180	2	8
β-strand	190-199	10	8
α-helix	200-204	5
β-strand	210-216	7	14
β-strand	219	1	15
β-strand	233	1	15
β-strand	235-241	7	14

Chain C: 10 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	60-88	29
α-helix	90-91	2
α-helix	93	1
β-strand	94-103	10	1
β-strand	111-118	8	1
β-strand	121-127	7	1
β-strand	130-133	4	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	2
α-helix	186-187	2
β-strand	188-193	6	3
β-strand	203-211	9	3
β-strand	212	1	2
β-strand	217-221	5	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 D: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	16
α-helix	4-5	2
β-strand	6-11	6	17
β-strand	21-30	10	17
β-strand	31	1	16
β-strand	36-41	6	18
β-strand	44-45	2	18
β-strand	50-51	2	17
β-strand	55-56	2	17
β-strand	62-70	9	17
β-strand	78-83	6	18
β-strand	91-94	4	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	C	protein	284	Homo sapiens	P15813 (AlphaFold model)
Human nkt TCR alpha chain	A	protein	220	Homo sapiens	K7N5M3 (AlphaFold model)
Human nkt TCR beta chain	B	protein	259	Homo sapiens	K7N5M4 (AlphaFold model)
Beta-2-microglobulin	D	protein	100	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>4EN3_1 Antigen-presenting glycoprotein CD1d (chains C)
ADPVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFS
DQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQ
GKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKS
ELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNA
DETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWHHHHHH

Sequence of entity 2 (A), FASTA

>4EN3_2 HUMAN NKT TCR ALPHA CHAIN (chains A)
ADLSQQGEEDPQALSIQEGENATMNCSYKTSINNLQWYRQNSGRGLVHLILIRSNEREKH
SGRLRVTLDTSKKSSSLLITASRAADTASYFCATYDRGSTLGRLYFGRGTQLTVWPDIQN
PDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVA
WSNKSDFACANAFNNSIIPEDTFFPSPESSSRGGLEVLFQ

Sequence of entity 3 (B), FASTA

>4EN3_3 HUMAN NKT TCR BETA CHAIN (chains B)
ADPEADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEK
GDLSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSENSGTGRIYEQYFGPGTRLTVTE
DLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQ
PLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIV
SAEAWGRADSRGGLEVLFQ

Sequence of entity 4 (D), FASTA

>4EN3_4 Beta-2-microglobulin (chains D)
PIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
FUC	alpha-L-fucopyranose	C6 H12 O5	1
AGH	N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}h…	C50 H99 N O9	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Water and common crystallization additives (GOL) are not listed.

Primary citation

The Molecular Basis for Recognition of CD1d/alpha-Galactosylceramide by a Human Non-Valpha24 T Cell Receptor Struct. Title. Lopez-Sagaseta, J., Kung, J.E., Savage, P.B. et al. PLoS Biol (2012) 10:e1001412-e1001412. DOI 10.1371/journal.pbio.1001412 · 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…
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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