7MX4: CD1c with antigen analogue 1

CD1c with antigen analogue 1. Determined by X-ray diffraction at 1.73 Å resolution. Released 17 Nov 2021.

Method: X-ray diffraction
Resolution: 1.73 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,413
Mol. weight: 46.11 kDa
Ligands: MLA, NHE, ZP7, D12
Released: 17 Nov 2021

Explore 7MX4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7MX4 contains 10 α-helices and 31 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	7-20	14	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	60-84	25
β-strand	94-105	12	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	138-150	13
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
β-strand	189-194	6	3
β-strand	202-212	11	3
β-strand	213	1	2
β-strand	218-223	6	4
β-strand	226-227	2	4
β-strand	232-233	2	3
β-strand	237-239	3	3
β-strand	243-253	11	3
β-strand	260-265	6	4
β-strand	274-277	4	4

Chain B: 3 helices, 12 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
β-strand	102	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein	A	protein	282	Homo sapiens	P29016 (AlphaFold model), P29017 (AlphaFold model)
Beta-2-microglobulin	B	protein	108	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7MX4_1 T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein (chains A)
ADASQEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLHQWSKGQFSN
EELSDLELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGGSPEGFFQVAFNG
LDLLSFQQTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFLLGLLDAGKM
YVHRQVRPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNA
NGTWYLRATLDVADGEAAGLSCRVKHSSLEGQDIILYWRGSL

Sequence of entity 2 (B), FASTA

>7MX4_2 Beta-2-microglobulin (chains B)
DAAIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFS
KDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGSLVPR

Ligands and cofactors

ID	Name	Formula	Copies
MLA	Malonic acid	C3 H4 O4	2
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	1
ZP7	(2S)-2,3-dihydroxypropyl hexadecanoate	C19 H38 O4	1
D12	Dodecane	C12 H26	1
ZPD	(4S,8R,12S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl…	C39 H79 O8 P	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Rational design of a hydrolysis-resistant mycobacterial phosphoglycolipid antigen presented by CD1c to T cells. Reijneveld, J.F., Marino, L., Cao, T.P. et al. J Biol Chem (2021) 297:101197-101197. DOI 10.1016/j.jbc.2021.101197 · 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
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
7MXF 2.0 Å, CD1c with antigen analogue 2

Browse structure collections

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