Annotations: 8IAK

Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3A-N71A) 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
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	WD40,CAF1C_H4-bd	e8iakB2	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40,CAF1C_H4-bd	ECOD (v295)
F	WD40,CAF1C_H4-bd	e8iakF2	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40,CAF1C_H4-bd	ECOD (v295)
A	WD40,CAF1C_H4-bd	e8iakA1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40,CAF1C_H4-bd	ECOD (v295)
E	WD40,CAF1C_H4-bd	e8iakE1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40,CAF1C_H4-bd	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth D], G [auth H]	PF04061	ORMDL family (ORMDL)	ORMDL family	-	Family
B, F	PF00155	Aminotransferase class I and II (Aminotran_1_2)	Aminotransferase class I and II		Domain
A, E	PF00155	Aminotransferase class I and II (Aminotran_1_2)	Aminotransferase class I and II		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth C], H [auth G]	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 [auth D], G [auth H]	Protein ORM2	identical protein binding protein binding binding	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
B, F	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
A, E	Long chain base biosynthesis protein 1,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 regulation of biological process regulation of cellular process biological regulation regulation of programmed cell death cell death programmed cell death developmental process multicellular organismal process reproductive system development reproductive process plant gross anatomical part developmental process developmental process involved in reproduction multicellular organism development fruit development embryo development ending in seed dormancy seed development anatomical structure development reproductive structure development post-embryonic development animal gross anatomical part developmental process system development growth cell growth multidimensional cell growth	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 plastid chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C [auth D], D [auth C], E A, B, C [auth D], D [auth C], E, F, G [auth H], H [auth G]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C [auth D], D [auth C], E A, B, C [auth D], D [auth C], E, F, G [auth H], H [auth G]	MemProtMD	Annotated as membrane protein by MemProtMD

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, F	LLP	Parent Component: LYS : AA0119 : N6-pyridoxal phosphate-L-lysine MOD:00128

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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.