6C15: CD1c

CD1c in complex with phosphatidylcholine. Determined by X-ray diffraction at 3.21 Å resolution. Released 21 Mar 2018.

Method: X-ray diffraction
Resolution: 3.21 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,875
Mol. weight: 46.98 kDa
Ligands: NAG, 6PL, D12
Released: 21 Mar 2018

Explore 6C15 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C15 contains 9 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: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	1
β-strand	24-32	9	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	52-55	4
α-helix	60-85	26
β-strand	94-103	10	1
β-strand	111-118	8	1
β-strand	122-127	6	1
β-strand	130-133	4	1
α-helix	138-150	13
α-helix	155-161	7
α-helix	162-166	5
α-helix	167-177	11
α-helix	179-182	4
β-strand	186	1	2
β-strand	189-196	8	3
β-strand	202-212	11	3
β-strand	213	1	2
β-strand	217-223	7	4
β-strand	226-227	2	4
β-strand	232-233	2	3
β-strand	237-238	2	3
β-strand	244-253	10	3
β-strand	260-266	7	4
β-strand	274-278	5	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	5
β-strand	16-21	6	6
β-strand	31-40	10	6
β-strand	41	1	5
β-strand	46-51	6	7
β-strand	54-55	2	7
β-strand	60-61	2	6
α-helix	62-64	3
β-strand	65-66	2	6
β-strand	72-80	9	6
β-strand	88-93	6	7
β-strand	101-104	4	7
α-helix	105-106	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1c	A	protein	287	Homo sapiens	P29017 (AlphaFold model)
Beta-2-microglobulin	B	protein	108	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6C15_1 T-cell surface glycoprotein CD1c (chains A)
ETGADASQEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLHNWSKGN
FSNEELSDLELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGKSPEGFFQVA
FNGLDLLSFQNTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFLLGLLDA
GKMYVHRQVRPEAWLSSRPSLGSGQLLLVCHASGFYPKPVWVTWMRNEQEQLGTKHGDIL
PNADGTWYLQVILEVASEEPAGLSCRVRHSSLGGQDIILYWGSLVPR

Sequence of entity 2 (B), FASTA

>6C15_2 Beta-2-microglobulin (chains B)
ETGIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFS
KDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGSLVPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
6PL	(4S,7R)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4…	C42 H85 N O8 P	1
D12	Dodecane	C12 H26	1

Water and common crystallization additives (NA, EDO, BME, SO4, MES) are not listed.

Primary citation

T cell autoreactivity directed toward CD1c itself rather than toward carried self lipids. Wun, K.S., Reijneveld, J.F., Cheng, T.Y. et al. Nat Immunol (2018) 19:397-406. DOI 10.1038/s41590-018-0065-7 · PubMed

Other PDB entries of the same protein (UniProt P29017 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MX4 1.73 Å, CD1c with antigen analogue 1
7MXF 2.0 Å, CD1c with antigen analogue 2
9QWJ 2.04 Å, Crystal structure of S2c TCR in complex with CD1c
7MXH 2.11 Å, CD1c with antigen analogue 3
9QWK 2.27 Å, Crystal structure of S2c-a5b6 TCR in complex with CD1c
5C9J 2.4 Å, Human CD1c with ligands in A' and F' channel
3OV6 2.5 Å, CD1c in complex with MPM (mannosyl-beta1-phosphomycoketide)
4ONO 2.71 Å, CD1c in complex with PM (phosphomycoketide)
6C09 2.95 Å, Ternary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex

Browse structure collections

About this viewer

MolViewer shows 6C15 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.