3SDX: Human autoreactive-Valpha24 NKT TCR

Crystal structure of human autoreactive-Valpha24 NKT TCR in complex with CD1d-beta-galactosylceramide. Determined by X-ray diffraction at 3.12 Å resolution. Released 5 Oct 2011.

Method: X-ray diffraction
Resolution: 3.12 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,830
Mol. weight: 189.34 kDa
Ligands: GCY
Released: 5 Oct 2011

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

Secondary structure: helices and β-sheets

3SDX contains 42 α-helices and 155 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: 8 helices, 20 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	62-88	27
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	141-149	9
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
β-strand	185	1	2
β-strand	188-193	6	3
β-strand	201-211	11	3
β-strand	212	1	2
β-strand	218-222	5	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	255	1	3
β-strand	260-263	4	4
β-strand	273-276	4	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
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
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
α-helix	95-96	2

Chain C: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	22
β-strand	24-32	9	22
β-strand	35-40	6	22
β-strand	48-49	2	22
α-helix	60-88	29
α-helix	90-91	2
α-helix	93	1
β-strand	94-104	11	22
α-helix	105	1
β-strand	110-118	9	22
β-strand	121-127	7	22
β-strand	130-133	4	22
α-helix	141-150	10
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-182	5
β-strand	185	1	23
β-strand	188-193	6	24
β-strand	201-211	11	24
β-strand	212	1	23
β-strand	218-220	3	25
β-strand	221-222	2	26
β-strand	225-226	2	26
β-strand	231-232	2	24
β-strand	236-237	2	24
α-helix	238	1
β-strand	243-252	10	24
β-strand	261-263	3	25
β-strand	273-275	3	25

Chain D: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	27
α-helix	4-5	2
β-strand	6-11	6	28
β-strand	21-30	10	28
β-strand	31	1	27
β-strand	36-41	6	29
β-strand	44-45	2	29
α-helix	46	1
β-strand	50-51	2	28
α-helix	52-54	3
β-strand	55-56	2	28
β-strand	62-70	9	28
β-strand	78-83	6	29
β-strand	91-94	4	29
α-helix	95-96	2

Chains E and G: 3 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	44-49	6	9
β-strand	56-58	3	8
β-strand	61-66	6	8
β-strand	71-76	6	8
α-helix	81-83	3
β-strand	85-92	8	9
β-strand	101-103	3	9
β-strand	107-112	6	9
β-strand	121-125	5	10
β-strand	126	1	11
β-strand	135-139	5	10
β-strand	155-157	3	10
α-helix	158-160	3
β-strand	161-165	5	10
β-strand	170-179	10	10
α-helix	186-189	4
β-strand	200	1	10

Chain F: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	9
β-strand	19-21	3	13
β-strand	22-25	4	12
β-strand	31-37	7	9
α-helix	42-43	2
β-strand	44-51	8	9
β-strand	54-57	4	9
β-strand	65-66	2	13
β-strand	70	1	12
β-strand	73	1	12
β-strand	76-78	3	13
α-helix	83-85	3
β-strand	87-95	9	9
β-strand	105-108	4	9
β-strand	112-117	6	9
β-strand	124	1	14
β-strand	127	1	15
β-strand	130-131	2	15
β-strand	132	1	11
α-helix	135-141	7
β-strand	143-153	11	15
β-strand	154	1	14
β-strand	158-164	7	16
β-strand	167-168	2	16
β-strand	173-175	3	15
α-helix	179	1
β-strand	180-181	2	15
β-strand	191-200	10	15
α-helix	201-205	5
β-strand	210-217	8	16
β-strand	220	1	17
α-helix	231-232	2
β-strand	234	1	17
β-strand	236-243	8	16

Chain H: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	30
β-strand	10-14	5	19
β-strand	19-21	3	31
β-strand	22-25	4	30
β-strand	31-37	7	19
α-helix	42-43	2
β-strand	44-51	8	19
β-strand	54-57	4	19
β-strand	65-66	2	31
β-strand	70	1	30
β-strand	73	1	30
β-strand	76-78	3	31
α-helix	83-85	3
β-strand	87-95	9	19
β-strand	105-108	4	19
β-strand	112-117	6	19
β-strand	124	1	32
β-strand	127-131	5	33
β-strand	132	1	21
α-helix	135-141	7
β-strand	143-153	11	33
β-strand	154	1	32
β-strand	158-164	7	34
β-strand	167-168	2	34
β-strand	173-175	3	33
β-strand	180-181	2	33
β-strand	191-200	10	33
α-helix	201-205	5
β-strand	210-217	8	34
β-strand	220	1	35
α-helix	231-232	2
β-strand	234	1	35
β-strand	236-243	8	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A, C	protein	275	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	99	Homo sapiens	P61769 (AlphaFold model)
NKT TCR Valpha24 chain	E, G	protein	204	Homo sapiens	P01848 (AlphaFold model)
NKT TCR autoreactive-Vbeta11 chain	F, H	protein	247	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>3SDX_1 Antigen-presenting glycoprotein CD1d (chains A, C)
RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWET
LQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILS
FQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQV
KPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYL
RATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWHHH

Sequence of entity 2 (B, D), FASTA

>3SDX_2 Beta-2-microglobulin (chains B, D)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, G), FASTA

>3SDX_3 NKT TCR Valpha24 chain (chains E, G)
NQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSNGR
YTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSP

Sequence of entity 4 (F, H), FASTA

>3SDX_4 NKT TCR autoreactive-Vbeta11 chain (chains F, H)
EADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGDL
SSESTVSRIRTEHFPLTLESARPSHTSQYLCASSEFGGTERTQETQYFGPGTRLLVLEDL
KNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPL
KEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSA
EAWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
GCY	N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosan…	C48 H93 N O8	2

Primary citation

Recognition of beta-linked self glycolipids mediated by natural killer T cell antigen receptors. Pellicci, D.G., Clarke, A.J., Patel, O. et al. Nat Immunol (2011) 12:827-833. DOI 10.1038/ni.2076 · 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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