1ONQ: CD1a

Crystal Structure of CD1a in Complex with a Sulfatide. Determined by X-ray diffraction at 2.15 Å resolution. Released 5 Aug 2003.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,791
Mol. weight: 92.32 kDa
Ligands: NAG, SLF, FUC
Released: 5 Aug 2003

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

Secondary structure: helices and β-sheets

1ONQ contains 24 α-helices and 60 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-20	13	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	60-88	29
α-helix	90-91	2
β-strand	94-105	12	1
β-strand	108-118	11	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	135-137	3
α-helix	139-148	10
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	188-194	7	3
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
α-helix	253-255	3
β-strand	259-264	6	4
α-helix	266-268	3
β-strand	273-276	4	4

Chains B and D: 2 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
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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	8
β-strand	24-32	9	8
β-strand	35-41	7	8
β-strand	46-49	4	8
α-helix	60-88	29
α-helix	90-91	2
β-strand	94-104	11	8
β-strand	109-118	10	8
β-strand	121-127	7	8
β-strand	130-133	4	8
α-helix	135-137	3
α-helix	139-148	10
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	9
β-strand	188-193	6	10
β-strand	201-211	11	10
β-strand	212	1	9
β-strand	217-222	6	11
β-strand	225-226	2	11
β-strand	231-232	2	10
β-strand	236-237	2	10
β-strand	243-252	10	10
α-helix	253-255	3
β-strand	259-264	6	11
α-helix	266-268	3
β-strand	273-276	4	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1a	A, C	protein	283	Homo sapiens	P06126 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	99	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1ONQ_1 T-cell surface glycoprotein CD1a (chains A, C)
ADGLKEPLSFHVIWIASFYNHSWKQNLVSGWLSDLQTHTWDSNSSTIVFLWPWSRGNFSN
EEWKELETLFRIRTIRSFEGIRRYAHELQFEYPFEIQVTGGCELHSGKVSGSFLQLAYQG
SDFVSFQNNSWLPYPVAGNMAKHFCKVLNQNQHENDITHNLLSDTCPRFILGLLDAGKAH
LQRQVKPEAWLSHGPSPGPGHLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQRGDILPSAD
GTWYLRATLEVAAGEAADLSCRVKHSSLEGQDIVLYWHHHHHH

Sequence of entity 2 (B, D), FASTA

>1ONQ_2 Beta-2-microglobulin (chains B, D)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
SLF	Sulfate-3-D-galactosyl-beta-1-1-N-stearoyl-D-sphingosine	C42 H81 N O11 S	2
FUC	alpha-L-fucopyranose	C6 H12 O5	2

Primary citation

Crystal structure of CD1a in complex with a sulfatide self antigen at a resolution of 2.15 A. Zajonc, D.M., Elsliger, M.A., Teyton, L. et al. Nat Immunol (2003) 4:808-815. DOI 10.1038/ni948 · PubMed

Other PDB entries of the same protein (UniProt P06126 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5J1A 1.86 Å, Antigen presenting molecule
4X6F 1.91 Å, CD1a binary complex with sphingomyelin
7SH4 2.0 Å, CD1a-phosphatidylglycerol binary structure
7KP1 2.02 Å, CD1a-42:2 SM binary complex
4X6E 2.1 Å, CD1a binary complex with lysophosphatidylcholine
9OHZ 2.14 Å, Crystal structure of CD1a presenting ganglioside GD3
6NUX 2.2 Å, CD1a-lipid binary complex
7KOZ 2.25 Å, CD1a-36:2 SM binary complex
7KP0 2.4 Å, CD1a-42:1 SM binary complex
7RYN 2.7 Å, CD1a-sulfatide-gdTCR complex
1XZ0 2.8 Å, Crystal structure of CD1a in complex with a synthetic mycobactin lipopeptide
4X6C 2.8 Å, CD1a ternary complex with lysophosphatidylcholine and BK6 TCR

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