5C9J: Human CD1c with ligands in A' and F' channel

Human CD1c with ligands in A' and F' channel. Determined by X-ray diffraction at 2.4 Å resolution. Released 2 Mar 2016.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,271
Mol. weight: 44.46 kDa
Ligands: PO4, STE, DAO
Released: 2 Mar 2016

Explore 5C9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C9J contains 12 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-23	14	1
β-strand	26-35	10	1
β-strand	38-44	7	1
β-strand	49-52	4	1
α-helix	63-88	26
α-helix	92-94	3
β-strand	97-108	12	1
β-strand	114-121	8	1
β-strand	124-129	6	1
β-strand	134-136	3	1
α-helix	137	1
α-helix	142-153	12
α-helix	156-164	9
α-helix	165-169	5
α-helix	170-185	16
β-strand	189	1	2
α-helix	190-191	2
β-strand	192-198	7	3
β-strand	205-215	11	3
β-strand	216	1	2
β-strand	221-226	6	4
β-strand	229-230	2	4
β-strand	235-236	2	3
β-strand	240-241	2	3
β-strand	247-256	10	3
β-strand	264-268	5	4
α-helix	270-272	3
β-strand	277-280	4	4

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 CD1c,T-cell surface glycoprotein CD1b	A	protein	281	Homo sapiens	P29016 (AlphaFold model), P29017 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5C9J_1 T-cell surface glycoprotein CD1c,T-cell surface glycoprotein CD1b (chains A)
EHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLHNWSKGNFSNEELSD
LELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGKSPEGFFQVAFNGLDLLS
FQNTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFLLGLLDAGKMYVHRQ
VKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNANWTWY
LRATLDVADGEAAGLSCRVKHSSLEGQDIILYWGPGSGGGL

Sequence of entity 2 (B), FASTA

>5C9J_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRD

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
STE	Stearic acid	C18 H36 O2	1
DAO	Lauric acid	C12 H24 O2	2

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

Primary citation

Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells. Mansour, S., Tocheva, A.S., Cave-Ayland, C. et al. Proc Natl Acad Sci U S A (2016) 113:E1266-E1275. DOI 10.1073/pnas.1519246113 · 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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