8DV3: Human CD1b presenting Phosphatidylinositol C34:1

Crystal structure of human CD1b presenting Phosphatidylinositol C34:1. Determined by X-ray diffraction at 1.9 Å resolution. Released 12 Apr 2023.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,592
Mol. weight: 49.59 kDa
Ligands: 6UL, PIE
Released: 12 Apr 2023

Explore 8DV3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DV3 contains 15 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-20	12	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	94-104	11	1
α-helix	105	1
β-strand	110-118	9	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	135-137	3
α-helix	138-148	11
α-helix	154-160	7
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	2
β-strand	188-195	8	3
β-strand	201-211	11	3
β-strand	212	1	2
β-strand	217-222	6	4
β-strand	225-226	2	4
β-strand	231-232	2	3
α-helix	234-235	2
β-strand	236-237	2	3
α-helix	238	1
β-strand	243-252	10	3
α-helix	253-255	3
β-strand	259-264	6	4
α-helix	266-268	3
β-strand	273-276	4	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	5
α-helix	6-7	2
β-strand	8-13	6	6
β-strand	23-32	10	6
β-strand	33	1	5
β-strand	38-43	6	7
β-strand	46-47	2	7
β-strand	52-53	2	6
α-helix	54-56	3
β-strand	57-58	2	6
β-strand	64-72	9	6
β-strand	80-85	6	7
α-helix	92	1
β-strand	93-96	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1b	A	protein	300	Homo sapiens	P29016 (AlphaFold model)
Beta-2-microglobulin	B	protein	101	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8DV3_1 T-cell surface glycoprotein CD1b (chains A)
HAFQGPTSFHVIQTSSFTNSTWAQTQGSGWLDDLQIHGWDSDSGTAIFLKPWSKGNFSDK
EVAELEEIFRVYIFGFAREVQDFAGDFQMKYPFEIQGIAGCELHSGGAIVSFLRGALGGL
DFLSVKNASCVPSPEGGSRAQKFCALIIQYQGIMETVRILLYETCPRYLLGVLNAGKADL
QRQVKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNANW
TWYLRATLDVADGEAAGLSCRVKHSSLEGQDIILYWRGSGLNDIFEAQKIEWHEHHHHHH

Sequence of entity 2 (B), FASTA

>8DV3_2 Beta-2-microglobulin (chains B)
PKIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSK
DWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
6UL	Tetracosyl palmitate	C40 H80 O2	1
PIE	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol	C43 H80 O13 P	1

Water and common crystallization additives (EDO, CL, IOD, NA) are not listed.

Primary citation

alpha beta T-cell receptor recognition of self-phosphatidylinositol presented by CD1b. Farquhar, R., Van Rhijn, I., Moody, D.B. et al. J Biol Chem (2023) 299:102849-102849. DOI 10.1016/j.jbc.2022.102849 · 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…
7MXF 2.0 Å, CD1c with antigen analogue 2

Browse structure collections

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