6C09: T-cell surface glycoprotein CD1c

Ternary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex. Determined by X-ray diffraction at 2.95 Å resolution. Released 21 Mar 2018.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,245
Mol. weight: 96.71 kDa
Ligands: NAG, EKG, D10
Released: 21 Mar 2018

Explore 6C09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C09 contains 28 α-helices and 72 β-strands across 4 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	8-20	13	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	60-85	26
β-strand	94-104	11	1
α-helix	109-110	2
β-strand	111-118	8	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	134	1
α-helix	140-151	12
α-helix	153-161	9
α-helix	162-166	5
α-helix	167-177	11
α-helix	179-182	4
β-strand	186	1	2
α-helix	187-188	2
β-strand	189-196	8	3
β-strand	203-212	10	3
β-strand	213	1	2
β-strand	217-223	7	4
β-strand	226-228	3	4
β-strand	232-233	2	3
α-helix	234-236	3
β-strand	237-238	2	3
β-strand	244-252	9	3
β-strand	260-266	7	4
α-helix	267-269	3
α-helix	272-273	2
β-strand	274-277	4	4

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-40	5	7
β-strand	45	1	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	79-83	5	7
β-strand	91-94	4	7
α-helix	95	1

Chain C: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	32-44	7	9
β-strand	51-57	7	9
β-strand	62-68	4	8
β-strand	71-76	6	8
β-strand	81-86	6	8
α-helix	91-93	3
β-strand	95-108	9	9
β-strand	111-114	4	9
α-helix	118	1
β-strand	121-126	6	9
α-helix	127-128	2
α-helix	130-132	3
β-strand	135-140	6	10
β-strand	141	1	11
β-strand	148-153	6	10
α-helix	162-164	3
β-strand	170-171	2	10
α-helix	172-175	4
β-strand	176-177	2	11
β-strand	188-192	5	10
α-helix	201-204	4
β-strand	214	1	10

Chain D: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-24	6	12
β-strand	31-44	7	13
β-strand	50-57	8	13
β-strand	60	1	13
β-strand	76-79	4	12
β-strand	86-90	5	12
α-helix	95-97	3
β-strand	99-107	8	13
β-strand	118-119	2	13
β-strand	123-128	6	13
α-helix	131-133	3
β-strand	135	1	14
β-strand	138-142	5	11
α-helix	143-145	3
α-helix	146-152	7
β-strand	154-164	11	11
β-strand	165	1	14
β-strand	169-175	7	15
β-strand	178-179	2	15
β-strand	184-186	3	11
β-strand	191-192	2	11
β-strand	202-211	10	11
α-helix	212-215	4
β-strand	221-228	8	15
β-strand	231	1	16
β-strand	245	1	16
β-strand	247-254	8	15

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)
3C8 T cell receptor alpha-chain	C	protein	205	Homo sapiens
3C8 T cell receptor beta-chain	D	protein	247	Homo sapiens

Sequence of entity 1 (A), FASTA

>6C09_1 T-cell surface glycoprotein CD1c (chains A)
ETGADASQEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLHNWSKGN
FSNEELSDLELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGKSPEGFFQVA
FNGLDLLSFQNTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFLLGLLDA
GKMYVHRQVRPEAWLSSRPSLGSGQLLLVCHASGFYPKPVWVTWMRNEQEQLGTKHGDIL
PNADGTWYLQVILEVASEEPAGLSCRVRHSSLGGQDIILYWGSLVPR

Sequence of entity 2 (B), FASTA

>6C09_2 Beta-2-microglobulin (chains B)
ETGIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFS
KDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGSLVPR

Sequence of entity 3 (C), FASTA

>6C09_3 3C8 T cell receptor alpha-chain (chains C)
MDQQVKQNSPSLSVQEGRISILNCDYTNSMFDYFLWYKKYPAEGPTFLISISSIKDKNED
GRFTVFLNKSAKHLSLHIVPSQPGDSAVYFCAASVGDKIIFGKGTRLHILPNMQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>6C09_4 3C8 T cell receptor beta-chain (chains D)
MGAGVSQSPSNKVTEKGKDVELRCDPISGHTALYWYRQSLGQGLEFLIYFQGNSAPDKSG
LPSDRFSAERTGGSVSTLTIQRTQQEDSAVYLCASSSYRGPRMNEQFFGPGTRLTVLEDL
KNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPL
KEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSA
EAWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
EKG	(2R)-2,3-dihydroxypropyl hexadecanoate	C19 H38 O4	1
D10	Decane	C10 H22	2

Water and common crystallization additives (K, EDO, PEG) 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)
6C15 3.21 Å, CD1c in complex with phosphatidylcholine

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