Crystal structure of bovine CD1d with bound C16:0-alpha-galactosyl ceramide. Determined by X-ray diffraction at 2.4 Å resolution. Released 14 Nov 2012.
Explore 4F7E in 3D Show helices and sheets RCSB PDB PDBe
4F7E contains 12 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.
| 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 | 60-86 | 27 | |
| β-strand | 94-104 | 11 | 1 |
| β-strand | 110-118 | 9 | 1 |
| β-strand | 121-127 | 7 | 1 |
| β-strand | 130-133 | 4 | 1 |
| α-helix | 134 | 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 | 231-232 | 2 | 3 |
| β-strand | 236-237 | 2 | 3 |
| β-strand | 243-252 | 10 | 3 |
| α-helix | 253-256 | 4 | |
| β-strand | 259-265 | 7 | 4 |
| β-strand | 273-276 | 4 | 4 |
| 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 |
| 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 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| CD1D antigen, d polypeptide | A | protein | 283 | Bos taurus | A1L565 (AlphaFold model) |
| Beta-2-microglobulin | B | protein | 98 | Bos taurus | P01888 (AlphaFold model) |
>4F7E_1 CD1D antigen, d polypeptide (chains A) SPAPQTPFSFQGLQISSFANRSWTRTDGLAWLGELQPYTWRNESDTIRFLKPWSRGTFSD QQWEQLQHTLLVYRSSFTRDIWEFVEKLHVEYPLEIQIATGCELLPRNISESFLRAAFQG RDVLSFQGMSWVSAPDAPPFIQEVIKVLNQNQGTKETVHWLLHDIWPELVRGVLQTGKSE LEKQVKPEAWLSSGPSPGPGRLLLVCHVSGFYPKPVRVMWMRGEQEEPGTRQGDVMPNAD STWYLRVTLDVAAGEVAGLSCQVKHSSLGDQDIILYWHHHHHH
>4F7E_2 Beta-2-microglobulin (chains B) IQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWS FYLLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDRDL
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
| 0SH | N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexad… | C40 H79 N O9 | 1 |
Water and common crystallization additives (SO4) are not listed.
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:
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