4MQ7: Human CD1d-sulfatide

Structure of human CD1d-sulfatide. Determined by X-ray diffraction at 2.6 Å resolution. Released 18 Dec 2013.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 2
Atoms: 3,079
Mol. weight: 44.74 kDa
Ligands: CIS, NAG
Released: 18 Dec 2013

Explore 4MQ7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4MQ7 contains 14 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
β-strand	24-32	9	1
β-strand	35-40	6	1
α-helix	47	1
β-strand	48-49	2	1
α-helix	60-87	28
α-helix	90-91	2
α-helix	93	1
β-strand	94-102	9	1
β-strand	112-118	7	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	140-148	9
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	2
β-strand	188-195	8	3
α-helix	196	1
β-strand	201-211	11	3
β-strand	212	1	2
β-strand	217-222	6	4
β-strand	225-226	2	4
β-strand	231-232	2	3
β-strand	236-237	2	3
β-strand	243-252	10	3
β-strand	259-264	6	4
α-helix	266-268	3
β-strand	273-276	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	35-41	7	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	78-84	7	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d, Cd1d1 protein	A	protein	281	Homo sapiens, Mus musculus	P11609 (AlphaFold model), P15813 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Mus musculus	P01887 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4MQ7_1 Antigen-presenting glycoprotein CD1d, Cd1d1 protein (chains A)
ADPVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFS
DQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQ
GKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKS
ELKKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNA
DETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWSGR

Sequence of entity 2 (B), FASTA

>4MQ7_2 Beta-2-microglobulin (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
CIS	(15Z)-N-((1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl…	C48 H91 N O11 S	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Crystal Structure of V delta 1 T Cell Receptor in Complex with CD1d-Sulfatide Shows MHC-like Recognition of a Self-Lipid by Human gamma delta T Cells. Luoma, A.M., Castro, C.D., Mayassi, T. et al. Immunity (2013) 39:1032-1042. DOI 10.1016/j.immuni.2013.11.001 · 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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