3GMP: Mouse CD1d

Structure of mouse CD1d in complex with PBS-25. Determined by X-ray diffraction at 1.7 Å resolution. Released 10 Nov 2009.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,591
Mol. weight: 47.74 kDa
Ligands: PBS, PLM, NAG
Released: 10 Nov 2009

Explore 3GMP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3GMP contains 13 α-helices and 30 β-strands across 2 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-20	13	1
β-strand	23-32	10	1
β-strand	35-40	6	1
α-helix	47	1
β-strand	48-49	2	1
α-helix	60-88	29
α-helix	93	1
α-helix	95	1
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	144-151	8
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	190-194	5	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	238-239	2	3
β-strand	245-253	9	3
β-strand	261-266	6	4
α-helix	268-270	3
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	36-41	6	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	78-83	6	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1d1	A	protein	287	Mus musculus	P11609 (AlphaFold model)
Beta-2 microglobulin	B	protein	99	Mus musculus	P01887 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3GMP_1 T-cell surface glycoprotein CD1d1 (chains A)
SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSN
QQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAF
QGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGK
SDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPN
ADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWGSHHHHHH

Sequence of entity 2 (B), FASTA

>3GMP_2 Beta-2 microglobulin (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
PBS	(2S,3S,4R)-N-octanoyl-1-[(alpha-D-galactopyranosyl)oxy]-2-amino-octadecane-3,4-…	C32 H63 N O9	1
PLM	Palmitic acid	C16 H32 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structural evaluation of potent NKT cell agonists: implications for design of novel stimulatory ligands. Schiefner, A., Fujio, M., Wu, D. et al. J Mol Biol (2009) 394:71-82. DOI 10.1016/j.jmb.2009.08.061 · 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
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
5EFI 1.8 Å, Crystal structure of mouse CD1d in complex with the p99p lipopeptide

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