6MJ6: MCD1d/xxx (JJ166) /iNKTCR ternary complex

Crystal structure of the mCD1d/xxx (JJ166) /iNKTCR ternary complex. Determined by X-ray diffraction at 2.45 Å resolution. Released 9 Jan 2019.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 6,896
Mol. weight: 97.45 kDa
Ligands: NAG, JTM
Released: 9 Jan 2019

Explore 6MJ6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MJ6 contains 24 α-helices and 69 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	9
β-strand	24-32	9	9
β-strand	35-40	6	9
α-helix	47	1
β-strand	48-49	2	9
α-helix	60-88	29
β-strand	96-107	12	9
β-strand	111-120	10	9
β-strand	123-129	7	9
β-strand	132-135	4	9
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	10
β-strand	190-197	8	11
β-strand	203-213	11	11
β-strand	214	1	10
β-strand	219-224	6	12
β-strand	227-228	2	12
β-strand	233-234	2	11
β-strand	238-239	2	11
β-strand	245-254	10	11
β-strand	261-266	6	12
β-strand	275-278	4	12

Chain B: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	36-41	6	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

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	45-50	6	2
β-strand	54-59	6	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	187-190	4
β-strand	201	1	3

Chain D: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-14	5	5
β-strand	19-25	7	4
β-strand	31-37	7	5
β-strand	44-49	6	5
β-strand	56-57	2	5
β-strand	65-67	3	4
β-strand	73-78	6	4
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	6
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	6
β-strand	152-158	7	7
β-strand	161-163	3	7
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	7
β-strand	214	1	8
α-helix	225-226	2
β-strand	228	1	8
β-strand	230-237	8	7

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	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	protein	241	Mus musculus, Homo sapiens	A0A5B9 (AlphaFold model), A0N8J3 (AlphaFold model), A2NTY6
Antigen-presenting glycoprotein CD1d1	A	protein	285	Mus musculus	P11609
Beta-2-microglobulin	B	protein	99	Mus musculus	P01887

Sequence of entity 1 (C), FASTA

>6MJ6_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,Human nkt tcr alpha chain (chains C)
MKTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSN
GRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (D), FASTA

>6MJ6_2 Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN (chains D)
MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGD
IPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTP
PKVSLFEPSKAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
A

Sequence of entity 3 (A), FASTA

>6MJ6_3 Antigen-presenting glycoprotein CD1d1 (chains A)
SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSN
QQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAF
QGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGK
SDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN
ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWHHHHHH

Sequence of entity 4 (B), FASTA

>6MJ6_4 Beta-2-microglobulin (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
JTM	N-[(2S,3S,4R)-1-({4-O-[(4-chlorophenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,…	C57 H104 Cl N O9	1

Water and common crystallization additives (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
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
6MIY 2.75 Å, Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex
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

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