3TZV: INKT TCR

Crystal structure of an iNKT TCR in complex with CD1d-lysophosphatidylcholine. Determined by X-ray diffraction at 3.06 Å resolution. Released 25 Apr 2012.

Method: X-ray diffraction
Resolution: 3.06 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,509
Mol. weight: 149.94 kDa
Ligands: LSC, HEX, D12
Released: 25 Apr 2012

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

Secondary structure: helices and β-sheets

3TZV contains 23 α-helices and 116 β-strands across 6 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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	9-13	5	2
β-strand	18-24	7	1
β-strand	31-37	7	2
β-strand	44-50	7	2
β-strand	55-58	4	1
β-strand	61-66	6	1
β-strand	71-76	6	1
α-helix	81-83	3
β-strand	85-92	8	2
β-strand	101-103	3	2
β-strand	107-112	6	2
β-strand	121-125	5	3
β-strand	127	1	4
β-strand	135-139	5	3
β-strand	150-152	3	3
β-strand	155-157	3	3
α-helix	158-160	3
β-strand	161-165	5	3
β-strand	170-179	10	3
α-helix	186-189	4
β-strand	198	1	3

Chain B: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	5
β-strand	10-14	5	6
β-strand	19-21	3	7
β-strand	22-25	4	5
β-strand	31-37	7	6
β-strand	44-49	6	6
β-strand	56-57	2	6
β-strand	64-66	3	7
β-strand	73	1	5
β-strand	76-78	3	7
α-helix	83-85	3
β-strand	87-94	8	6
β-strand	106-108	3	6
β-strand	112-117	6	6
β-strand	124	1	8
β-strand	127-131	5	4
α-helix	132-134	3
α-helix	135-141	7
β-strand	143-153	11	4
β-strand	154	1	8
β-strand	158-164	7	9
β-strand	167-168	2	9
β-strand	173-175	3	4
β-strand	180-181	2	4
β-strand	191-200	10	4
α-helix	201-204	4
β-strand	210-217	8	9
β-strand	220	1	10
α-helix	231-232	2
β-strand	234	1	10
β-strand	236-243	8	9

Chain C: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	11
β-strand	24-32	9	11
β-strand	35-40	6	11
β-strand	48-49	2	11
α-helix	60-88	29
β-strand	94-103	10	11
α-helix	109-110	2
β-strand	111-118	8	11
β-strand	122-127	6	11
β-strand	130-133	4	11
α-helix	141-150	10
α-helix	152-164	13
α-helix	166-181	16
β-strand	185	1	12
α-helix	186-187	2
β-strand	188-192	5	13
β-strand	204-212	9	13
β-strand	213	1	12
β-strand	218-222	5	14
β-strand	232-233	2	13
β-strand	237-238	2	13
β-strand	244-251	8	13
β-strand	261-265	5	14
β-strand	274-277	4	14

Chain D: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	15
β-strand	22-30	9	15
β-strand	36-41	6	16
β-strand	45	1	16
β-strand	50-51	2	15
α-helix	52-54	3
β-strand	55-56	2	15
β-strand	62-69	8	15
β-strand	78-83	6	16
β-strand	91-94	4	16
α-helix	95-96	2

Chain G: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
β-strand	9-13	5	2
β-strand	18-24	7	17
β-strand	31-37	7	2
β-strand	44-50	7	2
β-strand	55-58	4	17
β-strand	61-66	6	17
β-strand	71-76	6	17
α-helix	81-83	3
β-strand	85-92	8	2
β-strand	101-103	3	2
β-strand	107-112	6	2
β-strand	121-125	5	18
β-strand	127	1	19
β-strand	135-139	5	18
β-strand	156-157	2	18
α-helix	158-160	3
β-strand	161-165	5	18
β-strand	170-178	9	18
α-helix	186-189	4
β-strand	200	1	18

Chain H: 4 helices, 26 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	64-66	3	22
β-strand	73	1	20
β-strand	76-78	3	22
α-helix	83-85	3
β-strand	87-94	8	21
β-strand	106-108	3	21
β-strand	112-117	6	21
β-strand	124	1	23
β-strand	127-131	5	19
α-helix	132-134	3
α-helix	135-141	7
β-strand	143-153	11	19
β-strand	154	1	23
β-strand	158-164	7	24
β-strand	167-168	2	24
β-strand	173-175	3	19
β-strand	180-181	2	19
β-strand	191-200	10	19
α-helix	201-204	4
β-strand	210-217	8	24
β-strand	220	1	25
β-strand	234	1	25
β-strand	236-243	8	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Invariant Natural Killer T Cell Receptor chain A	A, G	protein	213	Homo sapiens
Invariant Natural Killer T Cell Receptor chain B	B, H	protein	259	Homo sapiens
Antigen-presenting glycoprotein CD1d	C	protein	276	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	D	protein	99	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A, G), FASTA

>3TZV_1 Invariant Natural Killer T Cell Receptor chain A (chains A, G)
MGKNQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKS
NGRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQN
PDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVA
WSNKSDFACANAFNNSIIPEDTFFPSPESSALE

Sequence of entity 2 (B, H), FASTA

>3TZV_2 Invariant Natural Killer T Cell Receptor chain B (chains B, H)
MSEADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKG
DLSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSEEGALKESVGTQYFGPGTRLLVLE
DLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQ
PLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIV
SAEAWGRADSVDKLAAALE

Sequence of entity 3 (C), FASTA

>3TZV_3 Antigen-presenting glycoprotein CD1d (chains C)
PVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSQDSDTVRSLKPWSQGTFSDQ
QWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGQASNNFFHVAFQGK
DILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLQGTCPQFVSGLLESGKSEL
KKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADE
TWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYW

Sequence of entity 4 (D), FASTA

>3TZV_4 Beta-2-microglobulin (chains D)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
LSC	(4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos…	C26 H53 N O7 P	1
HEX	Hexane	C6 H14	1
D12	Dodecane	C12 H26	1

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

Primary citation

Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor. Lopez-Sagaseta, J., Sibener, L.V., Kung, J.E. et al. EMBO J (2012) 31:2047-2059. DOI 10.1038/emboj.2012.54 · 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…

Browse structure collections

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