1ZT4: T-cell surface glycoprotein CD1d

The crystal structure of human CD1d with and without alpha-Galactosylceramide. Determined by X-ray diffraction at 3.0 Å resolution. Released 19 Jul 2005.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,093
Mol. weight: 88.25 kDa
Ligands: AGH
Released: 19 Jul 2005

Explore 1ZT4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ZT4 contains 17 α-helices and 52 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: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	10-20	11	1
β-strand	23-32	10	1
β-strand	35-40	6	1
β-strand	48-49	2	1
α-helix	60-87	28
β-strand	94-104	11	1
β-strand	110-118	9	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	140-148	9
α-helix	154-159	6
α-helix	160-165	6
α-helix	166-181	16
α-helix	186-187	2
β-strand	188-194	7	2
β-strand	203-211	9	2
β-strand	217-219	3	3
β-strand	231-232	2	2
β-strand	236-237	2	2
β-strand	243-250	8	2
β-strand	260-264	5	3
β-strand	273-276	4	3

Chains B and D: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	4
β-strand	21-30	10	4
β-strand	36-41	6	5
β-strand	44-45	2	5
α-helix	46	1
β-strand	50-51	2	4
β-strand	55-56	2	4
β-strand	62-70	9	4
β-strand	78-83	6	5
β-strand	92-94	3	5

Chain C: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	6
β-strand	24-32	9	6
β-strand	35-40	6	6
α-helix	47	1
β-strand	48-49	2	6
α-helix	60-87	28
α-helix	90-91	2
α-helix	93	1
β-strand	94-104	11	6
β-strand	110-118	9	6
β-strand	121-127	7	6
β-strand	130-133	4	6
α-helix	139-150	12
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-182	17
β-strand	188-194	7	7
β-strand	203-211	9	7
β-strand	217-219	3	8
β-strand	221-222	2	9
β-strand	225-226	2	9
β-strand	231-237	7	7
β-strand	243-249	7	7
α-helix	251-252	2
β-strand	260-261	2	10
β-strand	262-264	3	8
β-strand	275-276	2	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1d	A, C	protein	281	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1ZT4_1 T-cell surface glycoprotein CD1d (chains A, C)
AEVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSD
QQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQG
KDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSE
LKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNAD
ETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGGSY

Sequence of entity 2 (B, D), FASTA

>1ZT4_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
AGH	N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}h…	C50 H99 N O9	1

Primary citation

The crystal structure of human CD1d with and without alpha-galactosylceramide. Koch, M., Stronge, V.S., Shepherd, D. et al. Nat Immunol (2005) 6:819-826. DOI 10.1038/ni1225 · PubMed

Other PDB entries of the same protein (UniProt P15813 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RSE 1.76 Å, Human CD1d with lipid antigen bound
8SOS 2.33 Å, Human CD1d presenting sphingomyelin C24:1 in complex with VHH nanobody 1D17
6V7Y 2.4 Å, Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5
4WW2 2.48 Å, Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8,…
3HUJ 2.5 Å, Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant…
4WO4 2.5 Å, The molecular bases of Delta/Alpha beta T cell-mediated antigen recognition.
8SGM 2.5 Å, Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and…
4EN3 2.57 Å, Crystal structure of a human Valpha24(-) NKT TCR in complex with…
4MQ7 2.6 Å, Structure of human CD1d-sulfatide
6V7Z 2.75 Å, Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22
3U0P 2.8 Å, Crystal structure of human CD1d-lysophosphatidylcholine
8SGB 2.8 Å, Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and…

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