7YIU
Cryo-EM structure of the C6-ceramide-bound SPT-ORMDL3 complex
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0009058 | biological_process | biosynthetic process |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0004758 | molecular_function | serine C-palmitoyltransferase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005789 | cellular_component | endoplasmic reticulum membrane |
| B | 0006665 | biological_process | sphingolipid metabolic process |
| B | 0006686 | biological_process | sphingomyelin biosynthetic process |
| B | 0006688 | biological_process | glycosphingolipid biosynthetic process |
| B | 0009058 | biological_process | biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0017059 | cellular_component | serine palmitoyltransferase complex |
| B | 0030148 | biological_process | sphingolipid biosynthetic process |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0046512 | biological_process | sphingosine biosynthetic process |
| B | 0046513 | biological_process | ceramide biosynthetic process |
| B | 0060612 | biological_process | adipose tissue development |
| B | 0098554 | cellular_component | cytoplasmic side of endoplasmic reticulum membrane |
| B | 1904504 | biological_process | positive regulation of lipophagy |
| C | 0004758 | molecular_function | serine C-palmitoyltransferase activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005783 | cellular_component | endoplasmic reticulum |
| C | 0005789 | cellular_component | endoplasmic reticulum membrane |
| C | 0006665 | biological_process | sphingolipid metabolic process |
| C | 0006686 | biological_process | sphingomyelin biosynthetic process |
| C | 0006688 | biological_process | glycosphingolipid biosynthetic process |
| C | 0008104 | biological_process | intracellular protein localization |
| C | 0017059 | cellular_component | serine palmitoyltransferase complex |
| C | 0030148 | biological_process | sphingolipid biosynthetic process |
| C | 0046512 | biological_process | sphingosine biosynthetic process |
| C | 0046513 | biological_process | ceramide biosynthetic process |
| C | 0098554 | cellular_component | cytoplasmic side of endoplasmic reticulum membrane |
| D | 0002903 | biological_process | negative regulation of B cell apoptotic process |
| D | 0005515 | molecular_function | protein binding |
| D | 0005783 | cellular_component | endoplasmic reticulum |
| D | 0005789 | cellular_component | endoplasmic reticulum membrane |
| D | 0005886 | cellular_component | plasma membrane |
| D | 0006672 | biological_process | ceramide metabolic process |
| D | 0010508 | biological_process | positive regulation of autophagy |
| D | 0016020 | cellular_component | membrane |
| D | 0017059 | cellular_component | serine palmitoyltransferase complex |
| D | 0030667 | cellular_component | secretory granule membrane |
| D | 0035579 | cellular_component | specific granule membrane |
| D | 1900060 | biological_process | negative regulation of ceramide biosynthetic process |
| D | 1900182 | biological_process | positive regulation of protein localization to nucleus |
Functional Information from PROSITE/UniProt
| site_id | PS00599 |
| Number of Residues | 10 |
| Details | AA_TRANSFER_CLASS_2 Aminotransferases class-II pyridoxal-phosphate attachment site. TFTKSFGASG |
| Chain | Residue | Details |
| B | THR376-GLY385 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 56 |
| Details | Transmembrane: {"description":"Helical","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 69 |
| Details | Topological domain: {"description":"Cytoplasmic","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 73 |
| Details | Transmembrane: {"description":"Helical","evidences":[{"source":"PubMed","id":"33558762","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6M4N","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6M4O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7CQI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7CQK","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 7 |
| Details | Topological domain: {"description":"Lumenal","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 16 |
| Details | Region: {"description":"Important for ceramide level-sensing","evidences":[{"source":"PubMed","id":"37308477","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Hydroxyproline","evidences":[{"source":"PubMed","id":"36408842","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | Site: {"description":"Within the serine palmitoyltransferase (SPT) complex, defines the length of the acyl chain-binding pocket, determining the acyl-CoA substrate preference"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Phosphotyrosine; by ABL","evidences":[{"source":"PubMed","id":"23629659","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
