7SH4: CD1a-phosphatidylglycerol binary structure

CD1a-phosphatidylglycerol binary structure. Determined by X-ray diffraction at 2.0 Å resolution. Released 5 Oct 2022.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,469
Mol. weight: 46.55 kDa
Ligands: NAG, MW9
Released: 5 Oct 2022

Explore 7SH4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SH4 contains 16 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: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-20	11	1
β-strand	23-32	10	1
β-strand	35-41	7	1
α-helix	43-45	3
β-strand	46-49	4	1
α-helix	52-55	4
α-helix	60-84	25
α-helix	90-91	2
β-strand	94-102	9	1
β-strand	113-118	6	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	166-170	5
α-helix	174-181	8
β-strand	185	1	2
β-strand	188-193	6	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
α-helix	279-281	3

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
α-helix	47	1
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1a	A	protein	285	Homo sapiens	P06126 (AlphaFold model)
Beta-2-microglobulin	B	protein	108	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7SH4_1 T-cell surface glycoprotein CD1a (chains A)
ATGLKEPLSFHVIWIASFYNHSWKQNLVSGWLSDLQTHTWDSNSSTIVFLWPWSRGNFSN
EEWKELETLFRIRTIRSFEGIRRYAHELQFEYPFEIQVTGGCELHSGKVSGSFLQLAYQG
SDFVSFQNNSWLPYPVAGNMAKHFCKVLNQNQHENDITHNLLSDTCPRFILGLLDAGKAH
LQRQVKPEAWLSHGPSPGPGHLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQRGDILPSAD
GTWYLRATLEVAAGEAADLSCRVKHSSLEGQDIVLYWEGSLVPRG

Sequence of entity 2 (B), FASTA

>7SH4_2 Beta-2-microglobulin (chains B)
GIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGSLVPRGS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
MW9	(21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosp…	C42 H81 O10 P	1

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

Primary citation

Staphylococcal phosphatidylglycerol antigens activate human T cells via CD1a. Monnot, G.C., Wegrecki, M., Cheng, T.Y. et al. Nat Immunol (2023) 24:110-122. DOI 10.1038/s41590-022-01375-z · 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
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
1ONQ 2.15 Å, Crystal Structure of CD1a in Complex with a Sulfatide
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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