4ONO: CD1c

CD1c in complex with PM (phosphomycoketide). Determined by X-ray diffraction at 2.71 Å resolution. Released 8 Oct 2014.

Method: X-ray diffraction
Resolution: 2.71 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,069
Mol. weight: 45.82 kDa
Ligands: MLI, PMK
Released: 8 Oct 2014

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

Secondary structure: helices and β-sheets

4ONO contains 10 α-helices and 30 β-strands across 1 chain. 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, 30 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
α-helix	4-5	2
β-strand	6-11	6	2
β-strand	21-30	10	2
β-strand	31	1	1
β-strand	35-41	7	3
β-strand	44-45	2	3
β-strand	50-51	2	2
α-helix	52-54	3
β-strand	55-56	2	2
β-strand	62-70	9	2
β-strand	78-84	7	3
β-strand	91-95	5	3
α-helix	97-99	3
β-strand	122-133	12	4
β-strand	139-147	9	4
β-strand	150-156	7	4
β-strand	161-164	4	4
α-helix	175-197	23
β-strand	209-220	12	4
β-strand	225-233	9	4
β-strand	236-242	7	4
β-strand	245-248	4	4
α-helix	254-261	8
α-helix	262-266	5
α-helix	270-279	10
α-helix	282-296	15
β-strand	301	1	5
β-strand	304-309	6	6
β-strand	317-327	11	6
β-strand	328	1	5
β-strand	332-338	7	7
β-strand	341-342	2	7
α-helix	343	1
β-strand	347-348	2	6
β-strand	352-353	2	6
β-strand	359-368	10	6
α-helix	369-372	4
β-strand	375-381	7	7
β-strand	389-392	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin/T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric…	A	protein	395	Homo sapiens	P29016 (AlphaFold model), P29017 (AlphaFold model), P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4ONO_1 Beta-2-microglobulin/T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein (chains A)
PIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGGGGSGGSGSGGGSSADASQ
EHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLHQWSKGQFSNEELSD
LELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGGSPEGFFQVAFNGLDLLS
FQQTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFLLGLLDAGKMYVHRQ
VKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNAQGTWY
LRATLDVADGEAAGLSCRVKHSSLEGQDIILYWHH

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	3
PMK	(4R,8S,16S,20R)-4,8,12,16,20-pentamethylheptacosyl dihydrogen phosphate	C32 H67 O4 P	1

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

Primary citation

Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by alpha beta T cells. Roy, S., Ly, D., Li, N.S. et al. Proc Natl Acad Sci U S A (2014) 111:E4648-E4657. DOI 10.1073/pnas.1408549111 · PubMed

Other PDB entries of the same protein (UniProt P29016 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WL1 1.38 Å, Crystal Structure of Human CD1b in Complex with PG
8GLG 1.6 Å, Crystal Structure of Human CD1b in Complex with Phosphatidylethanolamine C34:1
5L2J 1.65 Å, Crystal Structure of human CD1b in complex with C36-GMM
5WKE 1.69 Å, Crystal Structure of Human CD1b in Complex with PS
6D64 1.7 Å, Crystal Structure of Human CD1b in Complex with POPC
7MX4 1.73 Å, CD1c with antigen analogue 1
2H26 1.8 Å, human CD1b in complex with endogenous phosphatidylcholine and spacer
8GLH 1.83 Å, Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5
9OI0 1.84 Å, Crystal structure of CD1b presenting ganglioside GD3
8GLE 1.85 Å, Crystal Structure of Human CD1b in Complex with Lysosulfatide
3T8X 1.9 Å, Crystal structure of human CD1b in complex with synthetic antigenic…
8DV3 1.9 Å, Crystal structure of human CD1b presenting Phosphatidylinositol C34:1

Browse structure collections

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