4F7C: Bovine CD1d with bound C12-di-sulfatide

Crystal structure of bovine CD1d with bound C12-di-sulfatide. Determined by X-ray diffraction at 2.86 Å resolution. Released 14 Nov 2012.

Method: X-ray diffraction
Resolution: 2.86 Å
Organism: Bos taurus
Chains: 4
Atoms: 6,216
Mol. weight: 92.18 kDa
Ligands: 0SG
Released: 14 Nov 2012

Explore 4F7C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4F7C contains 28 α-helices and 60 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
β-strand	24-32	9	1
β-strand	35-40	6	1
β-strand	48-49	2	1
α-helix	60-88	29
α-helix	90-91	2
α-helix	93	1
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	141-148	8
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	216-222	7	4
β-strand	225-226	2	4
α-helix	227	1
β-strand	230-232	3	3
β-strand	236-237	2	3
β-strand	243-252	10	3
β-strand	260-265	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	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	35-41	7	7
β-strand	44-45	2	7
β-strand	48-50	3	6
α-helix	51-53	3
β-strand	54-55	2	6
β-strand	61-69	9	6
β-strand	77-83	7	7
β-strand	90-93	4	7
α-helix	94-95	2

Chain C: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	8
β-strand	24-32	9	8
β-strand	35-40	6	8
β-strand	48-49	2	8
α-helix	60-88	29
α-helix	90-91	2
α-helix	93	1
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	141-148	8
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	203-211	9	10
β-strand	212	1	9
β-strand	217-222	6	11
β-strand	225-226	2	11
α-helix	227	1
β-strand	230-232	3	10
β-strand	236-237	2	10
β-strand	243-250	8	10
β-strand	259-264	6	11
α-helix	266-268	3
β-strand	273-277	5	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	48-50	3	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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD1D antigen, d polypeptide	A, C	protein	283	Bos taurus	A1L565 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	98	Bos taurus	P01888 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4F7C_1 CD1D antigen, d polypeptide (chains A, C)
SPAPQTPFSFQGLQISSFANRSWTRTDGLAWLGELQPYTWRNESDTIRFLKPWSRGTFSD
QQWEQLQHTLLVYRSSFTRDIWEFVEKLHVEYPLEIQIATGCELLPRNISESFLRAAFQG
RDVLSFQGMSWVSAPDAPPFIQEVIKVLNQNQGTKETVHWLLHDIWPELVRGVLQTGKSE
LEKQVKPEAWLSSGPSPGPGRLLLVCHVSGFYPKPVRVMWMRGEQEEPGTRQGDVMPNAD
STWYLRVTLDVAAGEVAGLSCQVKHSSLGDQDIILYWHHHHHH

Sequence of entity 2 (B, D), FASTA

>4F7C_2 Beta-2-microglobulin (chains B, D)
IQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWS
FYLLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDRDL

Ligands and cofactors

ID	Name	Formula	Copies
0SG	N-{(2S,3R,4E)-1-[(3,6-di-O-sulfo-beta-D-galactopyranosyl)oxy]-3-hydroxyoctadec-…	C36 H69 N O14 S2	2

Primary citation

Crystal Structures of Bovine CD1d Reveal Altered αGalCer Presentation and a Restricted A' Pocket Unable to Bind Long-Chain Glycolipids. Wang, J., Guillaume, J., Pauwels, N. et al. PLoS One (2012) 7:e47989-e47989. DOI 10.1371/journal.pone.0047989 · PubMed

Other PDB entries of the same protein (UniProt A1L565 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4F7E 2.4 Å, Crystal structure of bovine CD1d with bound C16:0-alpha-galactosyl ceramide

Browse structure collections

About this viewer

MolViewer shows 4F7C 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.