7KP1: CD1a-42:2 SM binary complex

CD1a-42:2 SM binary complex. Determined by X-ray diffraction at 2.02 Å resolution. Released 5 May 2021.

Method: X-ray diffraction
Resolution: 2.02 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,337
Mol. weight: 45.9 kDa
Ligands: FO4
Released: 5 May 2021

Explore 7KP1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KP1 contains 15 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	10-20	11	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	52-55	4
α-helix	60-84	25
α-helix	90-91	2
β-strand	94-103	10	1
β-strand	111-118	8	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	166-171	6
α-helix	174-181	8
β-strand	185	1	2
β-strand	188-193	6	3
α-helix	197-198	2
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
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	106	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7KP1_1 T-cell surface glycoprotein CD1a (chains A)
ATGLKEPLSFHVIWIASFYNHSWKQNLVSGWLSDLQTHTWDSNSSTIVFLWPWSRGNFSN
EEWKELETLFRIRTIRSFEGIRRYAHELQFEYPFEIQVTGGCELHSGKVSGSFLQLAYQG
SDFVSFQNNSWLPYPVAGNMAKHFCKVLNQNQHENDITHNLLSDTCPRFILGLLDAGKAH
LQRQVKPEAWLSHGPSPGPGHLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQRGDILPSAD
GTWYLRATLEVAAGEAADLSCRVKHSSLEGQDIVLYWEGSLVPRG

Sequence of entity 2 (B), FASTA

>7KP1_2 Beta-2-microglobulin (chains B)
AIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGSLVPR

Ligands and cofactors

ID	Name	Formula	Copies
FO4	sphingomyelin	C47 H94 N2 O6 P	1

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

Primary citation

CD1a selectively captures endogenous cellular lipids that broadly block T cell response. Cotton, R.N., Wegrecki, M., Cheng, T.Y. et al. J Exp Med (2021) 218. DOI 10.1084/jem.20202699 · 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
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

Browse structure collections

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