Annotations: 8C81

Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	Aminotran_1_2	e8c81E1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Aminotran_1_2	ECOD (v295)
C	Aminotran_1_2	e8c81C2	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Aminotran_1_2	ECOD (v295)
B	Aminotran_1_2	e8c81B1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Aminotran_1_2	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E	PF02383	SacI homology domain (Syja_N)	SacI homology domain	-	Family
C	PF00155	Aminotransferase class I and II (Aminotran_1_2)	Aminotransferase class I and II		Domain
B	PF00155	Aminotransferase class I and II (Aminotran_1_2)	Aminotransferase class I and II		Domain
A	PF04061	ORMDL family (ORMDL)	ORMDL family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	Phosphatidylinositol-3-phosphatase SAC1	phosphoric ester hydrolase activity phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity hydrolase activity, acting on ester bonds phosphatidylinositol bisphosphate phosphatase activity phosphatase activity hydrolase activity phosphatidylinositol-3,5-bisphosphate phosphatase activity phosphatidylinositol phosphate phosphatase activity catalytic activity phosphatidylinositol-3-phosphate phosphatase activity phosphatidylinositol monophosphate phosphatase activity phosphatidylinositol-4-phosphate phosphatase activity phosphatidylinositol phosphate 4-phosphatase activity	membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism phosphatidylinositol metabolic process dephosphorylation lipid modification primary metabolic process phosphatidylinositol dephosphorylation phospholipid dephosphorylation phosphate-containing compound metabolic process phosphorus metabolic process lipid metabolic process cellular homeostasis chemical homeostasis homeostatic process intracellular sphingolipid homeostasis intracellular chemical homeostasis lipid homeostasis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna endomembrane system Golgi stack membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna endomembrane system Golgi stack Golgi medial cisterna cell cortex cortical endoplasmic reticulum cell periphery endoplasmic reticulum subcompartment endoplasmic reticulum endoplasmic reticulum tubular network Golgi membrane membrane bounding membrane of organelle organelle membrane mitochondrial membrane organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex host intracellular membrane-bounded organelle host cellular component cytoplasmic viral factory host intracellular part other organism part host cell cytoplasm part host intracellular organelle host cell viral assembly compartment viral factory host cell cytoplasm host cell part host intracellular region nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane
D	Serine palmitoyltransferase-regulating protein TSC3	enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity	regulation of cellular process sphingolipid biosynthetic process regulation of lipid metabolic process positive regulation of biological process lipid biosynthetic process positive regulation of sphingolipid biosynthetic process regulation of primary metabolic process cellular component biogenesis positive regulation of metabolic process regulation of sphingolipid biosynthetic process positive regulation of biosynthetic process positive regulation of lipid metabolic process cellular component organization or biogenesis positive regulation of cellular process regulation of cellular process sphingolipid biosynthetic process regulation of lipid metabolic process positive regulation of biological process lipid biosynthetic process positive regulation of sphingolipid biosynthetic process regulation of primary metabolic process cellular component biogenesis positive regulation of metabolic process regulation of sphingolipid biosynthetic process positive regulation of biosynthetic process positive regulation of lipid metabolic process cellular component organization or biogenesis positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process sphingolipid metabolic process regulation of macromolecule metabolic process regulation of cellular component biogenesis macromolecule biosynthetic process biosynthetic process positive regulation of lipid biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process regulation of lipid biosynthetic process macromolecule metabolic process regulation of metabolic process lipid metabolic process cellular homeostasis chemical homeostasis homeostatic process intracellular sphingolipid homeostasis intracellular chemical homeostasis lipid homeostasis 3-keto-sphinganine metabolic process	serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane
C	Serine palmitoyltransferase 2	C-palmitoyltransferase activity acyltransferase activity serine C-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity palmitoyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding C-palmitoyltransferase activity acyltransferase activity serine C-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity palmitoyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding	polyol metabolic process sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process lipid biosynthetic process sphingolipid metabolic process primary metabolic process alcohol metabolic process diol biosynthetic process sphingosine metabolic process sphingoid metabolic process sphingosine biosynthetic process diol metabolic process biosynthetic process polyol biosynthetic process polyol metabolic process sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process lipid biosynthetic process sphingolipid metabolic process primary metabolic process alcohol metabolic process diol biosynthetic process sphingosine metabolic process sphingoid metabolic process sphingosine biosynthetic process diol metabolic process biosynthetic process polyol biosynthetic process alcohol biosynthetic process metabolic process cellular process small molecule metabolic process lipid metabolic process ceramide metabolic process ceramide biosynthetic process cellular homeostasis chemical homeostasis homeostatic process intracellular sphingolipid homeostasis intracellular chemical homeostasis lipid homeostasis	cellular anatomical structure membrane serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle cellular anatomical structure membrane serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system
B	Serine palmitoyltransferase 1	C-palmitoyltransferase activity acyltransferase activity serine C-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity palmitoyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding C-palmitoyltransferase activity acyltransferase activity serine C-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity palmitoyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding	polyol metabolic process sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process lipid biosynthetic process sphingolipid metabolic process primary metabolic process alcohol metabolic process diol biosynthetic process sphingosine metabolic process sphingoid metabolic process sphingosine biosynthetic process diol metabolic process biosynthetic process polyol biosynthetic process polyol metabolic process sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process lipid biosynthetic process sphingolipid metabolic process primary metabolic process alcohol metabolic process diol biosynthetic process sphingosine metabolic process sphingoid metabolic process sphingosine biosynthetic process diol metabolic process biosynthetic process polyol biosynthetic process alcohol biosynthetic process metabolic process cellular process small molecule metabolic process lipid metabolic process ceramide metabolic process ceramide biosynthetic process cellular homeostasis chemical homeostasis homeostatic process intracellular sphingolipid homeostasis intracellular chemical homeostasis lipid homeostasis	serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane
A	Protein ORM1	-	regulation of cellular process sphingolipid biosynthetic process regulation of lipid metabolic process negative regulation of biological process lipid biosynthetic process negative regulation of lipid biosynthetic process regulation of primary metabolic process cellular component biogenesis regulation of sphingolipid biosynthetic process negative regulation of cellular process cellular component organization or biogenesis negative regulation of sphingolipid biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process sphingolipid biosynthetic process regulation of lipid metabolic process negative regulation of biological process lipid biosynthetic process negative regulation of lipid biosynthetic process regulation of primary metabolic process cellular component biogenesis regulation of sphingolipid biosynthetic process negative regulation of cellular process cellular component organization or biogenesis negative regulation of sphingolipid biosynthetic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process sphingolipid metabolic process regulation of macromolecule metabolic process regulation of cellular component biogenesis macromolecule biosynthetic process biosynthetic process negative regulation of biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process regulation of lipid biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of lipid metabolic process lipid metabolic process ceramide metabolic process cellular homeostasis chemical homeostasis homeostatic process intracellular sphingolipid homeostasis intracellular chemical homeostasis lipid homeostasis response to stimulus response to topologically incorrect protein response to stress response to unfolded protein localization import into cell transport endocytosis establishment of localization vesicle-mediated transport	serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E	IPR002013	SAC domain	Domain
C	IPR001917	Aminotransferase, class-II, pyridoxal-phosphate binding site	Binding Site
C	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
C	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
C	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
C	IPR004839	Aminotransferase, class I/classII, large domain	Domain
C	IPR050087	8-amino-7-oxononanoate synthase class-II	Family
B	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
B	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
B	IPR004839	Aminotransferase, class I/classII, large domain	Domain
B	IPR050087	8-amino-7-oxononanoate synthase class-II	Family
A	IPR007203	ORMDL family	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	S-acyltransferases	Serine palmitoyltransferase (SPT) in complex with ORM1, monomer

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.