Annotations: 7YJM

Cryo-EM structure of the monomeric atSPT-ORM1 complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
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)
A	IMS	e7yjmA01	A: a/b three-layered sandwiches	X: Rossmann-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: IMS	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth C]	PF11779	Small subunit of serine palmitoyltransferase-like (SPT_ssu-like)	Small subunit of serine palmitoyltransferase-like	-	Family
C [auth D]	PF04061	ORMDL family (ORMDL)	ORMDL family	-	Family
B	PF00155	Aminotransferase class I and II (Aminotran_1_2)	Aminotransferase class I and II		Domain
A	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
E [auth C]	Transmembrane protein, putative (DUF3317)	protein-containing complex binding binding	regulation of cellular process sphingolipid biosynthetic process regulation of lipid metabolic process lipid biosynthetic process regulation of primary metabolic process cellular component biogenesis regulation of sphingolipid biosynthetic process cellular component organization or biogenesis regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process sphingolipid metabolic process regulation of macromolecule metabolic process regulation of cellular process sphingolipid biosynthetic process regulation of lipid metabolic process lipid biosynthetic process regulation of primary metabolic process cellular component biogenesis regulation of sphingolipid biosynthetic process cellular component organization or biogenesis 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 metabolic process cellular process regulation of macromolecule biosynthetic process regulation of lipid biosynthetic process macromolecule metabolic process regulation of metabolic process lipid metabolic process developmental process multicellular organism development multicellular organismal process gametophyte development anatomical structure development pollen development	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 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
D [auth E]	atLCB1	C-palmitoyltransferase activity acyltransferase activity serine C-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity C-acyltransferase activity catalytic activity palmitoyltransferase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding C-palmitoyltransferase activity acyltransferase activity serine C-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity C-acyltransferase activity catalytic activity palmitoyltransferase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding	regulation of biological process regulation of cellular process biological regulation cellular process regulation of programmed cell death cell death programmed cell death developmental process multicellular organismal process reproductive system development reproductive process embryo development developmental process involved in reproduction multicellular organism development regulation of biological process regulation of cellular process biological regulation cellular process regulation of programmed cell death cell death programmed cell death developmental process multicellular organismal process reproductive system development reproductive process embryo development 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 system development 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 small molecule metabolic process lipid metabolic process ceramide metabolic process ceramide biosynthetic process growth cell growth multidimensional cell growth	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 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]	ORMDL family protein	-	response to oxidative stress response to stimulus response to stress ceramide metabolic process sphingolipid metabolic process primary metabolic process metabolic process cellular process lipid metabolic process developmental process multicellular organismal process plant organ development plant organ senescence multicellular organism development response to oxidative stress response to stimulus response to stress ceramide metabolic process sphingolipid metabolic process primary metabolic process metabolic process cellular process lipid metabolic process developmental process multicellular organismal process plant organ development plant organ senescence multicellular organism development anatomical structure development leaf development leaf senescence shoot system development phyllome development system development defense response to bacterium biological process involved in interspecies interaction between organisms response to other organism defense response response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus sphingolipid biosynthetic process biosynthetic process lipid biosynthetic process cellular homeostasis chemical homeostasis homeostatic process intracellular sphingolipid homeostasis intracellular chemical homeostasis lipid homeostasis cellular response to stimulus cellular response to stress response to endoplasmic reticulum stress	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	Long chain base biosynthesis protein 2a	C-palmitoyltransferase activity acyltransferase activity serine C-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity C-acyltransferase activity catalytic activity palmitoyltransferase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding C-palmitoyltransferase activity acyltransferase activity serine C-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity C-acyltransferase activity catalytic activity palmitoyltransferase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding	regulation of biological process regulation of cellular process biological regulation cellular process regulation of programmed cell death cell death programmed cell death polyol metabolic process sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process lipid biosynthetic process sphingolipid metabolic process primary metabolic process regulation of biological process regulation of cellular process biological regulation cellular process regulation of programmed cell death cell death programmed cell death 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 small molecule metabolic process lipid metabolic process response to light stimulus developmental process multicellular organismal process response to stimulus response to red or far red light multicellular organism development photomorphogenesis anatomical structure development response to radiation response to abiotic stimulus post-embryonic development ceramide metabolic process ceramide biosynthetic process gametophyte development pollen development	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 vacuole 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 vacuole cytoplasm intracellular membrane-bounded organelle endoplasmic reticulum endomembrane system organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane
A	atLCB1	C-palmitoyltransferase activity acyltransferase activity serine C-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity C-acyltransferase activity catalytic activity palmitoyltransferase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding C-palmitoyltransferase activity acyltransferase activity serine C-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity C-acyltransferase activity catalytic activity palmitoyltransferase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding	regulation of biological process regulation of cellular process biological regulation cellular process regulation of programmed cell death cell death programmed cell death developmental process multicellular organismal process reproductive system development reproductive process embryo development developmental process involved in reproduction multicellular organism development regulation of biological process regulation of cellular process biological regulation cellular process regulation of programmed cell death cell death programmed cell death developmental process multicellular organismal process reproductive system development reproductive process embryo development 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 system development 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 small molecule metabolic process lipid metabolic process ceramide metabolic process ceramide biosynthetic process growth cell growth multidimensional cell growth	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 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 [auth C]	IPR024512	Small subunit of serine palmitoyltransferase-like	Family
D [auth E]	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
D [auth E]	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
D [auth E]	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
D [auth E]	IPR004839	Aminotransferase, class I/classII, large domain	Domain
D [auth E]	IPR050087	8-amino-7-oxononanoate synthase class-II	Family
C [auth D]	IPR007203	ORMDL family	Family
B	IPR001917	Aminotransferase, class-II, pyridoxal-phosphate binding site	Binding Site
B	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
B	IPR015422	Pyridoxal phosphate-dependent transferase, small 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	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A	IPR004839	Aminotransferase, class I/classII, large domain	Domain
A	IPR050087	8-amino-7-oxononanoate synthase class-II	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C [auth D], D [auth E], E [auth C]	OPM	Transmembrane	Alpha-helical polytopic	ORMDL family	ORMDL family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

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

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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.