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	0006672	biological_process	ceramide metabolic process
A	0006686	biological_process	sphingomyelin biosynthetic process
A	0006940	biological_process	regulation of smooth muscle contraction
A	0010508	biological_process	positive regulation of autophagy
A	0016020	cellular_component	membrane
A	0030148	biological_process	sphingolipid biosynthetic process
A	0030667	cellular_component	secretory granule membrane
A	0035339	cellular_component	SPOTS complex
A	0035579	cellular_component	specific granule membrane
A	0042552	biological_process	myelination
A	0044255	biological_process	cellular lipid metabolic process
A	0061744	biological_process	motor behavior
A	0090153	biological_process	regulation of sphingolipid biosynthetic process
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	0006665	biological_process	sphingolipid metabolic process
B	0006686	biological_process	sphingomyelin biosynthetic process
B	0009058	biological_process	biosynthetic process
B	0016020	cellular_component	membrane
B	0016746	molecular_function	acyltransferase activity
B	0017059	cellular_component	serine C-palmitoyltransferase complex
B	0030148	biological_process	sphingolipid biosynthetic process
B	0030170	molecular_function	pyridoxal phosphate binding
B	0035339	cellular_component	SPOTS complex
B	0046511	biological_process	sphinganine biosynthetic process
B	0046512	biological_process	sphingosine biosynthetic process
B	0046513	biological_process	ceramide biosynthetic process
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	0006665	biological_process	sphingolipid metabolic process
E	0008104	biological_process	protein localization
E	0016020	cellular_component	membrane
E	0017059	cellular_component	serine C-palmitoyltransferase complex
E	0030148	biological_process	sphingolipid biosynthetic process
E	0046512	biological_process	sphingosine biosynthetic process
E	0046513	biological_process	ceramide biosynthetic process
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	0006665	biological_process	sphingolipid metabolic process
S	0006686	biological_process	sphingomyelin biosynthetic process
S	0009058	biological_process	biosynthetic process
S	0016020	cellular_component	membrane
S	0016746	molecular_function	acyltransferase activity
S	0017059	cellular_component	serine C-palmitoyltransferase complex
S	0030148	biological_process	sphingolipid biosynthetic process
S	0030170	molecular_function	pyridoxal phosphate binding
S	0035339	cellular_component	SPOTS complex
S	0046511	biological_process	sphinganine biosynthetic process
S	0046512	biological_process	sphingosine biosynthetic process
S	0046513	biological_process	ceramide biosynthetic process
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	0005783	cellular_component	endoplasmic reticulum
T	0005789	cellular_component	endoplasmic reticulum membrane
T	0006665	biological_process	sphingolipid metabolic process
T	0006686	biological_process	sphingomyelin biosynthetic process
T	0009058	biological_process	biosynthetic process
T	0016020	cellular_component	membrane
T	0016740	molecular_function	transferase activity
T	0016746	molecular_function	acyltransferase activity
T	0017059	cellular_component	serine C-palmitoyltransferase complex
T	0030148	biological_process	sphingolipid biosynthetic process
T	0030170	molecular_function	pyridoxal phosphate binding
T	0046511	biological_process	sphinganine biosynthetic process
T	0046512	biological_process	sphingosine biosynthetic process
T	0046513	biological_process	ceramide biosynthetic process
T	0060612	biological_process	adipose tissue development
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	24
Details	TOPO_DOM: Cytoplasmic => ECO:0000255

Chain	Residue	Details
E	MET1-GLN12
E	GLN58-GLN71
A	PRO140-TYR153

site_id	SWS_FT_FI2
Number of Residues	38
Details	TRANSMEM: Helical => ECO:0000255

Chain	Residue	Details
E	MET13-LEU29
E	THR35-PRO57
A	PHE101-THR117
A	ILE122-LEU139

site_id	SWS_FT_FI3
Number of Residues	4
Details	TOPO_DOM: Lumenal => ECO:0000255

Chain	Residue	Details
E	GLU30-ARG34
B	ARG37-LEU473

site_id	SWS_FT_FI4
Number of Residues	1
Details	SITE: Within the serine palmitoyltransferase (SPT) complex, defines the length of the acyl chain-binding pocket, determining the acyl-CoA substrate preference

Chain	Residue	Details
B	TYR164
E	MET28

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