3L9R: Bovine CD1b3 with endogenously bound ligands

Crystal structure of bovine CD1b3 with endogenously bound ligands. Determined by X-ray diffraction at 2.3 Å resolution. Released 16 Jun 2010.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Bos taurus
Chains: 8
Atoms: 12,721
Mol. weight: 182.01 kDa
Ligands: L9R, L9Q, NAG
Released: 16 Jun 2010

Explore 3L9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3L9R contains 55 α-helices and 121 β-strands across 8 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: 11 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	60-83	24
β-strand	94-103	10	1
β-strand	111-118	8	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	138-148	11
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	2
α-helix	186-187	2
β-strand	188-193	6	3
β-strand	201-211	11	3
β-strand	212	1	2
β-strand	217-222	6	4
β-strand	225-226	2	4
α-helix	227	1
β-strand	231-232	2	3
α-helix	233-235	3
β-strand	236-237	2	3
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

Chains B and F: 3 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	36-41	6	7
β-strand	44-45	2	7
α-helix	46-47	2
β-strand	49-50	2	6
α-helix	51-53	3
β-strand	54-55	2	6
β-strand	61-69	9	6
β-strand	77-82	6	7
β-strand	90-93	4	7

Chain C: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	8
β-strand	24-25	2	8
β-strand	29-32	4	8
β-strand	35-41	7	8
β-strand	46-49	4	8
α-helix	60-84	25
β-strand	94-103	10	8
β-strand	111-118	8	8
β-strand	121-127	7	8
β-strand	130-133	4	8
α-helix	134	1
α-helix	138-148	11
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	9
α-helix	186-187	2
β-strand	188-193	6	10
β-strand	202-211	10	10
β-strand	212	1	9
β-strand	217-222	6	11
β-strand	225-226	2	11
β-strand	231-232	2	10
α-helix	233-235	3
β-strand	236-237	2	10
β-strand	243-251	9	10
α-helix	253-255	3
β-strand	259-264	6	11
α-helix	266-268	3
β-strand	273-276	4	11

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
β-strand	49-50	2	13
α-helix	51-53	3
β-strand	54-55	2	13
β-strand	61-69	9	13
β-strand	77-82	6	14
α-helix	89	1
β-strand	90-93	4	14

Chain E: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-20	12	15
β-strand	23-32	10	15
β-strand	35-41	7	15
β-strand	46-49	4	15
α-helix	60-84	25
β-strand	94-103	10	15
β-strand	111-118	8	15
β-strand	121-127	7	15
β-strand	130-133	4	15
α-helix	134	1
α-helix	138-148	11
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	16
α-helix	186-187	2
β-strand	188-194	7	17
β-strand	201-211	11	17
β-strand	212	1	16
β-strand	217-222	6	18
β-strand	225-226	2	18
α-helix	227	1
β-strand	231-232	2	17
α-helix	233-235	3
β-strand	236-237	2	17
β-strand	243-252	10	17
α-helix	253-255	3
β-strand	259-264	6	18
α-helix	266-268	3
β-strand	273-276	4	18

Chain G: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	22
β-strand	24-32	9	22
β-strand	35-41	7	22
β-strand	46-49	4	22
α-helix	60-83	24
β-strand	94-103	10	22
β-strand	111-118	8	22
β-strand	121-127	7	22
β-strand	130-133	4	22
α-helix	138-148	11
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	23
α-helix	186-187	2
β-strand	188-193	6	24
β-strand	201-211	11	24
β-strand	212	1	23
β-strand	217-222	6	25
β-strand	225-226	2	25
β-strand	231-232	2	24
α-helix	233-235	3
β-strand	236-237	2	24
β-strand	243-252	10	24
α-helix	253-255	3
β-strand	259-264	6	25
α-helix	266-268	3
β-strand	273-276	4	25

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	26
α-helix	4-5	2
β-strand	6-11	6	27
β-strand	21-30	10	27
β-strand	31	1	26
β-strand	35-41	7	28
β-strand	44-45	2	28
β-strand	49-50	2	27
α-helix	51-53	3
β-strand	54-55	2	27
β-strand	61-69	9	27
β-strand	77-83	7	28
β-strand	90-93	4	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD1b3	A, C, E, G	protein	283	Bos taurus	Q1L1H6 (AlphaFold model)
Beta-2-microglobulin	B, D, F, H	protein	98	Bos taurus	P01888 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3L9R_1 CD1b3 (chains A, C, E, G)
EDVFQGPTSFHLMQISTFVNSTWAQNQGSGWLDDLQIHGWESDSGTAIFLKPWSKGNFSD
DEVTELVDLFRAYFIGFTREVQDRVNEFQLEYPFVIQVTAGCELHSGEAIESSLRGALGG
LDFVSIQNHSCVPAPDSGSRGQKFCALTTQYQGISDIIERLLSETCPRYLLGVLDAGKAE
LQRQVKPEAWLSSGPTPGPGRLLLVCHVSGFYPKPVRVMWMRGEQEQPGTQQGDLMPNAD
WTWYLRVTLNVAAGEAAGLNCRVKHSSLGDQDIILYWHHHHHH

Sequence of entity 2 (B, D, F, H), FASTA

>3L9R_2 Beta-2-microglobulin (chains B, D, F, H)
IQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWS
FYLLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDRDL

Ligands and cofactors

ID	Name	Formula	Copies
L9R	(2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C44 H86 N O8 P	2
L9Q	(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl…	C41 H80 N O8 P	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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

Primary citation

Crystal structure of bovine CD1b3 with endogenously bound ligands. Girardi, E., Wang, J., Mac, T.T. et al. J Immunol (2010) 185:376-386. DOI 10.4049/jimmunol.1000042 · PubMed

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