6MIY: MCD1d/xxa (JJ239)/iNKTCR ternary complex

Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex. Determined by X-ray diffraction at 2.75 Å resolution. Released 9 Jan 2019.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Mus musculus, Homo sapiens
Chains: 8
Atoms: 13,394
Mol. weight: 193.98 kDa
Ligands: JTV
Released: 9 Jan 2019

Explore 6MIY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MIY contains 48 α-helices and 144 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	8	1
β-strand	9-18	10	10
β-strand	24-32	9	10
β-strand	35-40	6	10
β-strand	48-49	2	10
α-helix	60-88	29
β-strand	96-107	12	10
β-strand	111-120	10	10
β-strand	123-129	7	10
β-strand	132-135	4	10
α-helix	141-143	3
α-helix	144-150	7
α-helix	154-162	9
α-helix	163-167	5
α-helix	168-178	11
α-helix	180-183	4
β-strand	187	1	11
β-strand	190-197	8	12
β-strand	204-213	10	12
β-strand	214	1	11
β-strand	219-224	6	13
β-strand	228	1	13
β-strand	233-234	2	12
β-strand	238-239	2	12
α-helix	240	1
β-strand	245-253	9	12
β-strand	261-266	6	13
β-strand	275-278	4	13

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	6-11	6	14
β-strand	21-30	10	14
β-strand	36-41	6	15
β-strand	44-45	2	15
α-helix	46	1
β-strand	50-51	2	14
α-helix	52-54	3
β-strand	55-56	2	14
β-strand	62-70	9	14
β-strand	78-83	6	15
β-strand	91-94	4	15

Chain C: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	32-38	7	2
β-strand	44-50	7	2
β-strand	56-59	4	1
β-strand	62-67	6	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	86-93	8	2
α-helix	100-101	2
β-strand	102-104	3	2
β-strand	108-113	6	2
β-strand	122-128	7	3
β-strand	135-140	6	3
α-helix	149-151	3
β-strand	157-158	2	3
α-helix	159-161	3
β-strand	162-166	5	3
α-helix	167-169	3
β-strand	171-179	9	3
α-helix	187-189	3
β-strand	201	1	3

Chain D: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-14	5	5
β-strand	19-21	3	6
β-strand	22-25	4	4
β-strand	31-37	7	5
β-strand	44-49	6	5
β-strand	56-57	2	5
β-strand	65-67	3	6
β-strand	73	1	4
β-strand	75-78	4	6
α-helix	83-85	3
β-strand	87-94	8	5
β-strand	101-102	2	5
β-strand	106-111	6	5
β-strand	118	1	7
α-helix	119-120	2
β-strand	121-126	6	3
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	3
β-strand	148	1	7
β-strand	152-158	7	8
β-strand	161-163	3	8
β-strand	167-169	3	3
α-helix	173	1
β-strand	174-175	2	3
β-strand	185-194	10	3
α-helix	195-199	5
α-helix	203	1
β-strand	204-211	8	8
β-strand	214	1	9
α-helix	225-226	2
β-strand	228	1	9
β-strand	230-237	8	8

Chain E: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	16
β-strand	24-32	9	16
β-strand	35-40	6	16
α-helix	47	1
β-strand	48-49	2	16
α-helix	60-88	29
β-strand	96-107	12	16
β-strand	111-120	10	16
β-strand	123-129	7	16
β-strand	132-135	4	16
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	17
β-strand	190-196	7	18
β-strand	203-213	11	18
β-strand	214	1	17
β-strand	219-224	6	19
β-strand	227-228	2	19
β-strand	233-234	2	18
β-strand	238-239	2	18
α-helix	240	1
β-strand	245-254	10	18
β-strand	261-266	6	19
β-strand	275-278	4	19

Chain F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	30
α-helix	4-5	2
β-strand	6-11	6	31
β-strand	21-30	10	31
β-strand	31	1	30
β-strand	36-41	6	32
β-strand	44-45	2	32
α-helix	46	1
β-strand	50-51	2	31
α-helix	52-54	3
β-strand	55-56	2	31
β-strand	62-70	9	31
β-strand	78-83	6	32
β-strand	91-94	4	32

Chain G: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	20
β-strand	10-14	5	21
β-strand	19-25	7	20
β-strand	32-38	7	21
β-strand	44-50	7	21
β-strand	54-59	6	20
β-strand	62-67	6	20
β-strand	72-77	6	20
α-helix	82-84	3
β-strand	86-93	8	21
β-strand	102-104	3	21
β-strand	108-113	6	21
β-strand	122	1	22
β-strand	124-128	5	23
β-strand	135-138	4	23
α-helix	149-151	3
β-strand	157-158	2	23
α-helix	159-161	3
β-strand	162-166	5	24
β-strand	171-175	5	24
β-strand	177-179	3	23
β-strand	201	1	22

Chain H: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	25
β-strand	10-14	5	26
β-strand	19-25	7	25
β-strand	31-37	7	26
β-strand	44-49	6	26
β-strand	56-57	2	26
β-strand	65-67	3	25
β-strand	73-78	6	25
α-helix	83-85	3
β-strand	87-94	8	26
β-strand	101-102	2	26
β-strand	106-111	6	26
β-strand	118	1	27
α-helix	119-120	2
β-strand	121-126	6	23
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	23
β-strand	148	1	27
β-strand	152-158	7	28
β-strand	161-163	3	28
β-strand	167-169	3	23
α-helix	173	1
β-strand	174-175	2	23
β-strand	185-194	10	23
α-helix	195-199	5
β-strand	204-211	8	28
β-strand	214	1	29
α-helix	225-226	2
β-strand	228	1	29
β-strand	230-237	8	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining…	C, G	protein	209	Mus musculus, Homo sapiens	A0A0B4J1J9 (AlphaFold model), K7N5M3 (AlphaFold model)
Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN	D, H	protein	241	Mus musculus, Homo sapiens	A0A5B9 (AlphaFold model), A0N8J3 (AlphaFold model), A2NTY6
Antigen-presenting glycoprotein CD1d1	A, E	protein	285	Mus musculus	P11609
Beta-2-microglobulin	B, F	protein	99	Mus musculus	P01887

Sequence of entity 1 (C, G), FASTA

>6MIY_1 T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN (chains C, G)
MKTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSN
GRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (D, H), FASTA

>6MIY_2 Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN (chains D, H)
MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGD
IPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTP
PKVSLFEPSKAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
A

Sequence of entity 3 (A, E), FASTA

>6MIY_3 Antigen-presenting glycoprotein CD1d1 (chains A, E)
SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSN
QQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAF
QGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGK
SDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN
ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWHHHHHH

Sequence of entity 4 (B, F), FASTA

>6MIY_4 Beta-2-microglobulin (chains B, F)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
JTV	N-{(2S,3S,4R)-1-[(4-O-benzyl-alpha-D-galactopyranosyl)oxy]-3,4-dihydroxyoctadec…	C57 H105 N O9	2

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

Primary citation

4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies. Janssens, J., Bitra, A., Wang, J. et al. ChemMedChem (2019) 14:147-168. DOI 10.1002/cmdc.201800649 · PubMed

Other PDB entries of the same protein (UniProt A0A0B4J1J9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MJJ 1.93 Å, Crystal structure of the mCD1d/xxm (JJ290) /iNKTCR ternary complex
6MJ4 2.0 Å, Crystal structure of MCD1D/INKTCR TERNARY COMPLEX bound to glycolipid (XXW)
6MIV 2.05 Å, Crystal structure of the mCD1d/xxq (JJ300)/iNKTCR ternary complex
6MJI 2.3 Å, Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex
6MJA 2.35 Å, Crystal structure of the mCD1d/xxo (JJ294) /iNKTCR ternary complex
6MJ6 2.45 Å, Crystal structure of the mCD1d/xxx (JJ166) /iNKTCR ternary complex
4Y16 2.6 Å, Crystal structure of the mCD1d/NC-aGC/iNKTCR ternary complex
8T4Z 2.69 Å, T-cell receptor and lipid complex structure
4ZAK 2.82 Å, Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex
4Y4K 2.9 Å, Crystal structure of the mCD1d/EF77/iNKTCR ternary complex
6MJQ 3.0 Å, Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex
4Y2D 3.05 Å, Crystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex

Browse structure collections

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