8T4Z: T-cell receptor and lipid complex structure

T-cell receptor and lipid complex structure. Determined by X-ray diffraction at 2.69 Å resolution. Released 7 Aug 2024.

Method: X-ray diffraction
Resolution: 2.69 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 6,649
Mol. weight: 98.46 kDa
Ligands: Y73
Released: 7 Aug 2024

Explore 8T4Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T4Z contains 23 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	24-32	9	1
β-strand	35-40	6	1
β-strand	48-49	2	1
α-helix	60-88	29
β-strand	96-107	12	1
β-strand	111-120	10	1
β-strand	123-129	7	1
β-strand	132-135	4	1
α-helix	136	1
α-helix	141-143	3
α-helix	144-152	9
α-helix	154-162	9
α-helix	163-167	5
α-helix	168-178	11
α-helix	180-183	4
β-strand	187	1	2
β-strand	190-197	8	3
β-strand	203-213	11	3
β-strand	214	1	2
β-strand	219-224	6	4
β-strand	227-228	2	4
β-strand	233-234	2	3
β-strand	238-239	2	3
β-strand	245-254	10	3
β-strand	261-266	6	4
α-helix	268-270	3
β-strand	275-278	4	4
α-helix	282-289	8

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	21-28	8	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
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 4 helices, 17 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	53-58	6	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	87-93	7	9
β-strand	104-106	3	9
β-strand	110-115	6	9
β-strand	124-130	7	10
β-strand	137-142	6	10
α-helix	148-151	4
β-strand	158-160	3	10
β-strand	164-168	5	10
α-helix	169-171	3
β-strand	173-182	10	10
α-helix	189-191	3
β-strand	203	1	10

Chain D: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-14	5	12
β-strand	19-21	3	13
β-strand	22-25	4	11
β-strand	31-38	8	12
β-strand	41-49	9	12
β-strand	56-57	2	12
β-strand	66-68	3	13
β-strand	74	1	11
β-strand	76-79	4	13
α-helix	84-86	3
β-strand	88-95	8	12
β-strand	102-108	2	12
β-strand	113-117	5	12
α-helix	120-122	3
β-strand	124	1	14
α-helix	125-126	2
β-strand	127-132	6	10
α-helix	133-134	2
α-helix	135-141	7
β-strand	143-153	11	10
β-strand	154	1	14
β-strand	158-164	7	15
β-strand	167-169	3	15
β-strand	173-175	3	10
β-strand	180-181	2	10
α-helix	189-190	2
β-strand	191-200	10	10
α-helix	201-204	4
β-strand	210-217	8	15
β-strand	220	1	16
β-strand	234	1	16
β-strand	236-243	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d1	A	protein	302	Mus musculus	P11609 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Mus musculus	P01887 (AlphaFold model)
T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera	C	protein	207	Mus musculus, Homo sapiens	A0A0B4J1J9 (AlphaFold model), K7N5M3 (AlphaFold model)
Beta-chain, T cell receptor beta chain MC.7.G5 chimera	D	protein	242	Mus musculus	A2NTY6, P0DTU4

Sequence of entity 1 (A), FASTA

>8T4Z_1 Antigen-presenting glycoprotein CD1d1 (chains A)
SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSN
QQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAF
QGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGK
SDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN
ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHHH
HH

Sequence of entity 2 (B), FASTA

>8T4Z_2 Beta-2-microglobulin (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (C), FASTA

>8T4Z_3 T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera (chains C)
TQVEQSPQSLVVRQGENSVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGR
YSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>8T4Z_4 Beta-chain, T cell receptor beta chain MC.7.G5 chimera (chains D)
MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGD
IPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

ID	Name	Formula	Copies
Y73	N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide	C42 H81 N O3	1

Primary citation

Lipidomic scanning of self-lipids identifies headless antigens for natural killer T cells. Cheng, T.Y., Praveena, T., Govindarajan, S. et al. Proc Natl Acad Sci U S A (2024) 121:e2321686121-e2321686121. DOI 10.1073/pnas.2321686121 · PubMed

Other PDB entries of the same protein (UniProt P11609 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3G08 1.6 Å, Crystal structure of the alpha-galactosylceramide analog OCH in complex with mouse CD1d
3GMO 1.6 Å, Structure of mouse CD1d in complex with C8PhF
6C6F 1.67 Å, Structure of glycolipid aGSA[26,P5p] in complex with mouse CD1d
3GML 1.7 Å, Structure of mouse CD1d in complex with C6Ph
3GMN 1.7 Å, Structure of mouse CD1d in complex with C10Ph
3GMP 1.7 Å, Structure of mouse CD1d in complex with PBS-25
3T1F 1.7 Å, Crystal structure of the mouse CD1d-Glc-DAG-s2 complex
5TW2 1.75 Å, Structure of mouse CD1d with bound alpha-galactosylsphingamide JG168
6C6J 1.79 Å, Structure of glycolipid aGSA[8,P5p] in complex with mouse CD1d
2FIK 1.8 Å, Structure of a microbial glycosphingolipid bound to mouse CD1d
3GMM 1.8 Å, Structure of mouse CD1d in complex with C8Ph
3GMQ 1.8 Å, Structure of mouse CD1d expressed in SF9 cells, no ligand added

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