5VCJ: Antigen-presenting glycoprotein CD1d1

Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR. Determined by X-ray diffraction at 3.16 Å resolution. Released 4 Apr 2018.

Method: X-ray diffraction
Resolution: 3.16 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 6,511
Mol. weight: 96.61 kDa
Ligands: NAG, PLM, N57
Released: 4 Apr 2018

Explore 5VCJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VCJ contains 20 α-helices and 71 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: 7 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	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	190-195	6	3
β-strand	204-213	10	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	238-240	3	3
β-strand	244-253	10	3
β-strand	261-266	6	4
β-strand	275-278	4	4

Chain B: 3 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	21-30	10	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
α-helix	52-54	3
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: 3 helices, 17 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	44-50	7	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	122-128	7	10
β-strand	135-140	6	10
α-helix	148-151	4
β-strand	156-158	3	10
α-helix	159-161	3
β-strand	162-166	5	10
β-strand	171-180	10	10
β-strand	201	1	10

Chain D: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
β-strand	31-37	7	12
β-strand	44-49	6	12
β-strand	56-57	2	12
β-strand	65-67	3	11
β-strand	73-78	6	11
α-helix	83-85	3
β-strand	87-94	8	12
β-strand	101-102	2	12
β-strand	106-111	6	12
β-strand	118	1	13
α-helix	119-120	2
β-strand	121-126	6	10
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	10
β-strand	148	1	13
β-strand	152-158	7	14
β-strand	161-162	2	14
β-strand	167-169	3	10
α-helix	173	1
β-strand	174-175	2	10
β-strand	185-194	10	10
α-helix	195-199	5
β-strand	204-211	8	14
β-strand	214	1	15
α-helix	225-226	2
β-strand	228	1	15
β-strand	230-237	8	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d1	A	protein	285	Mus musculus	P11609 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Mus musculus	P01887 (AlphaFold model)
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)	C	protein	209	Mus musculus, Homo sapiens	A0A0B4J1J9 (AlphaFold model), K7N5M3 (AlphaFold model)
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)	D	protein	241	Mus musculus, Homo sapiens

Sequence of entity 1 (A), FASTA

>5VCJ_1 Antigen-presenting glycoprotein CD1d1 (chains A)
SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSN
QQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAF
QGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGK
SDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN
ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWHHHHHH

Sequence of entity 2 (B), FASTA

>5VCJ_2 Beta-2-microglobulin (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (C), FASTA

>5VCJ_3 Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain) (chains C)
MKTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSN
GRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>5VCJ_4 Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain) (chains D)
MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGD
IPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTP
PKVSLFEPSKAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
A

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
PLM	Palmitic acid	C16 H32 O2	1
N57	(2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside	C24 H49 N O8	1

Primary citation

Enhancing T cell responses and tumour immunity by vaccination with peptides conjugated to a weak NKT cell agonist. Compton, B.J., Farrand, K.J., Tang, C.W. et al. Org Biomol Chem (2019) 17:1225-1237. DOI 10.1039/c8ob02982b · 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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