Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6M4O

Cryo-EM structure of the monomeric SPT-ORMDL3 complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0002903	biological_process	negative regulation of B cell apoptotic process
A	0005515	molecular_function	protein binding
A	0005783	cellular_component	endoplasmic reticulum
A	0005789	cellular_component	endoplasmic reticulum membrane
A	0005886	cellular_component	plasma membrane
A	0006665	biological_process	sphingolipid metabolic process
A	0006672	biological_process	ceramide metabolic process
A	0010508	biological_process	positive regulation of autophagy
A	0016020	cellular_component	membrane
A	0017059	cellular_component	serine palmitoyltransferase complex
A	0030148	biological_process	sphingolipid biosynthetic process
A	0030667	cellular_component	secretory granule membrane
A	0035579	cellular_component	specific granule membrane
A	0090156	biological_process	intracellular sphingolipid homeostasis
A	1900060	biological_process	negative regulation of ceramide biosynthetic process
A	1900182	biological_process	positive regulation of protein localization to nucleus
A	2000303	biological_process	regulation of ceramide biosynthetic process
B	0004758	molecular_function	serine C-palmitoyltransferase activity
B	0005515	molecular_function	protein binding
B	0005783	cellular_component	endoplasmic reticulum
B	0005789	cellular_component	endoplasmic reticulum membrane
B	0006629	biological_process	lipid metabolic process
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	0016746	molecular_function	acyltransferase activity
B	0017059	cellular_component	serine palmitoyltransferase complex
B	0030148	biological_process	sphingolipid biosynthetic process
B	0030170	molecular_function	pyridoxal phosphate binding
B	0043604	biological_process	amide biosynthetic process
B	0046512	biological_process	sphingosine biosynthetic process
B	0046513	biological_process	ceramide biosynthetic process
B	0098554	cellular_component	cytoplasmic side of endoplasmic reticulum membrane
B	1904504	biological_process	positive regulation of lipophagy
B	1904649	biological_process	regulation of fat cell apoptotic process
E	0004758	molecular_function	serine C-palmitoyltransferase activity
E	0005515	molecular_function	protein binding
E	0005783	cellular_component	endoplasmic reticulum
E	0005789	cellular_component	endoplasmic reticulum membrane
E	0006629	biological_process	lipid metabolic process
E	0006665	biological_process	sphingolipid metabolic process
E	0006686	biological_process	sphingomyelin biosynthetic process
E	0006688	biological_process	glycosphingolipid biosynthetic process
E	0008104	biological_process	intracellular protein localization
E	0017059	cellular_component	serine palmitoyltransferase complex
E	0030148	biological_process	sphingolipid biosynthetic process
E	0046512	biological_process	sphingosine biosynthetic process
E	0046513	biological_process	ceramide biosynthetic process
E	0098554	cellular_component	cytoplasmic side of endoplasmic reticulum membrane
S	0004758	molecular_function	serine C-palmitoyltransferase activity
S	0005515	molecular_function	protein binding
S	0005783	cellular_component	endoplasmic reticulum
S	0005789	cellular_component	endoplasmic reticulum membrane
S	0006629	biological_process	lipid metabolic process
S	0006665	biological_process	sphingolipid metabolic process
S	0006686	biological_process	sphingomyelin biosynthetic process
S	0006688	biological_process	glycosphingolipid biosynthetic process
S	0009058	biological_process	biosynthetic process
S	0016740	molecular_function	transferase activity
S	0016746	molecular_function	acyltransferase activity
S	0017059	cellular_component	serine palmitoyltransferase complex
S	0030148	biological_process	sphingolipid biosynthetic process
S	0030170	molecular_function	pyridoxal phosphate binding
S	0043604	biological_process	amide biosynthetic process
S	0046512	biological_process	sphingosine biosynthetic process
S	0046513	biological_process	ceramide biosynthetic process
S	0098554	cellular_component	cytoplasmic side of endoplasmic reticulum membrane
S	1904504	biological_process	positive regulation of lipophagy
S	1904649	biological_process	regulation of fat cell apoptotic process
T	0004758	molecular_function	serine C-palmitoyltransferase activity
T	0005515	molecular_function	protein binding
T	0005789	cellular_component	endoplasmic reticulum membrane
T	0006629	biological_process	lipid metabolic process
T	0006665	biological_process	sphingolipid metabolic process
T	0006686	biological_process	sphingomyelin biosynthetic process
T	0006688	biological_process	glycosphingolipid biosynthetic process
T	0009058	biological_process	biosynthetic process
T	0016740	molecular_function	transferase activity
T	0016746	molecular_function	acyltransferase activity
T	0017059	cellular_component	serine palmitoyltransferase complex
T	0030148	biological_process	sphingolipid biosynthetic process
T	0030170	molecular_function	pyridoxal phosphate binding
T	0046512	biological_process	sphingosine biosynthetic process
T	0046513	biological_process	ceramide biosynthetic process
T	0060612	biological_process	adipose tissue development
T	0098554	cellular_component	cytoplasmic side of endoplasmic reticulum membrane
T	1904504	biological_process	positive regulation of lipophagy

Functional Information from PDB Data

site_id	AC1
Number of Residues	14
Details	binding site for residue PLP T 601

Chain	Residue
S	PHE337
T	HIS347
T	THR376
T	THR378
T	LYS379
T	GLY385
S	ALA339
T	GLY238
T	PHE239
T	HIS263
T	SER265
T	GLU315
T	ASP344
T	ALA346

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
T	THR376-GLY385

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Modified residue: {"description":"Phosphotyrosine; by ABL","evidences":[{"source":"PubMed","id":"23629659","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	36
Details	Transmembrane: {"description":"Helical","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1
Details	Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"evidenceCode":"ECO:0000250"}]}

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	36
Details	Topological domain: {"description":"Cytoplasmic","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	7
Details	Topological domain: {"description":"Lumenal","evidences":[{"evidenceCode":"ECO:0000255"}]}

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

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)