4Y4F: MCD1d/GCK127/iNKTCR ternary complex

Crystal structure of the mCD1d/GCK127/iNKTCR ternary complex. Determined by X-ray diffraction at 3.19 Å resolution. Released 27 May 2015.

Method: X-ray diffraction
Resolution: 3.19 Å
Organisms: Mus musculus, Homo sapiens
Chains: 8
Atoms: 12,597
Mol. weight: 191.84 kDa
Ligands: 49M, NAG
Released: 27 May 2015

Explore 4Y4F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y4F contains 44 α-helices and 146 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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	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	96-106	11	1
β-strand	112-120	9	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	190-196	7	3
β-strand	205-213	9	3
β-strand	214	1	2
β-strand	219-224	6	4
β-strand	227-228	2	4
β-strand	232-234	3	3
β-strand	238-239	2	3
β-strand	245-252	8	3
β-strand	262-266	5	4
β-strand	275-278	4	4

Chain B: 1 helix, 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	35-41	7	7
β-strand	44-45	2	7
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	78-84	7	7
β-strand	91-94	4	7

Chain C: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	32-38	7	9
β-strand	45-50	6	9
β-strand	54-59	6	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-93	8	9
β-strand	102-104	3	9
β-strand	108-113	6	9
β-strand	122-127	6	10
β-strand	128	1	11
β-strand	135-140	6	10
α-helix	149-151	3
β-strand	156-158	3	10
α-helix	159-161	3
β-strand	162-166	5	10
α-helix	167-169	3
β-strand	171-180	10	10
α-helix	187-189	3
β-strand	201	1	10

Chain D: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	22-25	4	12
β-strand	31-37	7	13
β-strand	44-49	6	13
β-strand	56-57	2	13
β-strand	65-67	3	14
β-strand	73	1	12
β-strand	75-78	4	14
α-helix	83-85	3
β-strand	87-94	8	13
β-strand	101-102	2	13
β-strand	106-111	6	13
β-strand	118	1	15
β-strand	121-125	5	11
α-helix	126-128	3
α-helix	129-135	7
β-strand	137-147	11	11
β-strand	148	1	15
β-strand	152-158	7	16
β-strand	161-163	3	16
β-strand	167-169	3	11
α-helix	173	1
β-strand	174-175	2	11
β-strand	185-194	10	11
α-helix	195-198	4
β-strand	204-211	8	16
β-strand	214	1	17
α-helix	225-226	2
β-strand	228	1	17
β-strand	230-237	8	16

Chain E: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	18
β-strand	24-32	9	18
β-strand	35-40	6	18
α-helix	47	1
β-strand	48-49	2	18
α-helix	60-88	29
β-strand	96-106	11	18
β-strand	112-120	9	18
β-strand	123-129	7	18
β-strand	132-135	4	18
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	19
β-strand	190-196	7	20
β-strand	205-213	9	20
β-strand	214	1	19
β-strand	219-224	6	21
β-strand	227-228	2	21
β-strand	232-234	3	20
β-strand	238-239	2	20
β-strand	245-252	8	20
β-strand	262-266	5	21
β-strand	275-278	4	21

Chain F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	22
α-helix	4-5	2
β-strand	6-11	6	23
β-strand	21-30	10	23
β-strand	31	1	22
β-strand	36-41	6	24
β-strand	44-45	2	24
β-strand	50-51	2	23
α-helix	52-54	3
β-strand	55-56	2	23
β-strand	62-70	9	23
β-strand	78-83	6	24
α-helix	90	1
β-strand	91-94	4	24

Chain G: 5 helices, 18 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	32-38	7	26
β-strand	44-50	7	26
β-strand	54-59	6	25
β-strand	62-67	6	25
β-strand	72-77	6	25
α-helix	82-84	3
β-strand	86-93	8	26
β-strand	102-104	3	26
β-strand	108-113	6	26
β-strand	122-127	6	27
β-strand	128	1	28
β-strand	135-140	6	27
α-helix	149-151	3
β-strand	156-158	3	27
α-helix	159-161	3
β-strand	162-166	5	27
α-helix	167-169	3
β-strand	171-180	10	27
α-helix	187-189	3
β-strand	201	1	27

Chain H: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	29
β-strand	10-14	5	30
β-strand	19-25	7	29
β-strand	31-37	7	30
β-strand	44-49	6	30
β-strand	56-57	2	30
β-strand	64-67	4	29
β-strand	73-78	6	29
α-helix	83-85	3
β-strand	87-94	8	30
β-strand	101-102	2	30
β-strand	106-111	6	30
β-strand	118	1	31
α-helix	119-120	2
β-strand	121-125	5	28
α-helix	126-128	3
α-helix	129-135	7
β-strand	137-147	11	28
β-strand	148	1	31
β-strand	152-158	7	32
β-strand	161-163	3	32
β-strand	167-169	3	28
α-helix	173	1
β-strand	174-175	2	28
β-strand	185-194	10	28
α-helix	195-199	5
β-strand	204-211	8	32
β-strand	214	1	33
α-helix	225-226	2
β-strand	228	1	33
β-strand	230-237	8	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d1	A, E	protein	285	Mus musculus	P11609 (AlphaFold model)
Beta-2-microglobulin	B, F	protein	99	Mus musculus	P01887 (AlphaFold model)
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain)	C, G	protein	209	Mus musculus, Homo sapiens	A0A0B4J1J9 (AlphaFold model), P01848 (AlphaFold model)
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)	D, H	protein	241	Mus musculus, Homo sapiens	A0A5B9, A2NTY6

Sequence of entity 1 (A, E), FASTA

>4Y4F_1 Antigen-presenting glycoprotein CD1d1 (chains A, E)
SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSN
QQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAF
QGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGK
SDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN
ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWHHHHHH

Sequence of entity 2 (B, F), FASTA

>4Y4F_2 Beta-2-microglobulin (chains B, F)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (C, G), FASTA

>4Y4F_3 Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain) (chains C, G)
MKTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSN
GRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D, H), FASTA

>4Y4F_4 Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain) (chains D, H)
MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGD
IPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTP
PKVSLFEPSKAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
A

Ligands and cofactors

ID	Name	Formula	Copies
49M	(1R)-1,5-anhydro-1-[(1E,3S,4S,5R)-4,5-dihydroxy-3-(nonacosanoylamino)nonadec-1-…	C54 H105 N O8	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structural modifications of alphaGalCer in both lipid and carbohydrate moiety influence activation of murine and human iNKT cells. Birkholz, A., Nemcovic, M., Yu, E.D. et al. To be published.

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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