6M4O | pdb_00006m4o

Cryo-EM structure of the monomeric SPT-ORMDL3 complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
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)
A [auth S]	F_UNCLASSIFIED	e6m4oS2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: F_UNCLASSIFIED	ECOD (1.6)
A [auth S]	Aminotran_5_N	e6m4oS1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth E]	PF11779	Small subunit of serine palmitoyltransferase-like (SPT_ssu-like)	Small subunit of serine palmitoyltransferase-like	-	Family
B [auth T]	PF00155	Aminotransferase class I and II (Aminotran_1_2)	Aminotransferase class I and II		Domain
A [auth S], E [auth B]	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 E]	Serine palmitoyltransferase small subunit A	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	localization macromolecule localization intracellular protein localization membrane lipid metabolic 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 localization macromolecule localization intracellular protein localization membrane lipid metabolic 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 membrane lipid biosynthetic process lipid metabolic process ceramide metabolic process amide biosynthetic process ceramide biosynthetic process amide 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 A]	ORM1-like protein 3	-	regulation of localization regulation of biological process regulation of protein localization positive regulation of protein localization to nucleus biological regulation positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus localization macromolecule localization protein localization to organelle positive regulation of protein localization intracellular protein localization behavior regulation of localization regulation of biological process regulation of protein localization positive regulation of protein localization to nucleus biological regulation positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus localization macromolecule localization protein localization to organelle positive regulation of protein localization intracellular protein localization behavior multicellular organismal process motor behavior myelination developmental process multicellular organism development axon ensheathment ensheathment of neurons anatomical structure development cellular process nervous system development system development regulation of amide metabolic 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 amide metabolic process regulation of ceramide biosynthetic process negative regulation of sphingolipid biosynthetic process regulation of biosynthetic process membrane lipid metabolic process ceramide metabolic process regulation of membrane lipid metabolic process negative regulation of amide metabolic process negative regulation of metabolic process primary metabolic process sphingolipid metabolic process amide biosynthetic process regulation of macromolecule metabolic process regulation of cellular component biogenesis macromolecule biosynthetic process negative regulation of ceramide biosynthetic process biosynthetic process negative regulation of biosynthetic process ceramide biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of lipid biosynthetic process macromolecule metabolic process membrane lipid biosynthetic process regulation of metabolic process negative regulation of lipid metabolic process lipid metabolic process sphingomyelin biosynthetic process phospholipid biosynthetic process phospholipid metabolic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process sphingomyelin metabolic process system process regulation of system process muscle contraction muscle system process regulation of muscle system process smooth muscle contraction regulation of smooth muscle contraction regulation of muscle contraction regulation of multicellular organismal process positive regulation of autophagy catabolic process autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process process utilizing autophagic mechanism positive regulation of cellular process cellular homeostasis chemical homeostasis homeostatic process intracellular sphingolipid homeostasis intracellular chemical homeostasis lipid homeostasis regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process regulation of B cell apoptotic process negative regulation of programmed cell death leukocyte apoptotic process regulation of apoptotic process B cell apoptotic process regulation of programmed cell death cell death negative regulation of B cell apoptotic process lymphocyte apoptotic process negative regulation of apoptotic process negative regulation of leukocyte apoptotic process apoptotic process programmed cell death negative regulation of lymphocyte apoptotic process	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule cell periphery plasma membrane serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex endoplasmic reticulum organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane
B [auth T]	Serine palmitoyltransferase 2	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	developmental process connective tissue development adipose tissue development animal organ development anatomical structure development tissue development membrane lipid metabolic process polyol metabolic process sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process lipid biosynthetic process sphingolipid metabolic process primary metabolic process developmental process connective tissue development adipose tissue development animal organ development anatomical structure development tissue development membrane lipid metabolic 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 membrane lipid biosynthetic process lipid metabolic process sphinganine metabolic process sphinganine biosynthetic process ceramide metabolic process amide biosynthetic process ceramide biosynthetic process amide metabolic process sphingomyelin biosynthetic process phospholipid biosynthetic process phospholipid metabolic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process sphingomyelin metabolic process positive regulation of autophagy regulation of biological process catabolic process regulation of cellular process lipophagy macroautophagy autophagy biological regulation positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of macroautophagy positive regulation of lipophagy regulation of lipophagy positive regulation of macroautophagy process utilizing autophagic mechanism regulation of metabolic process positive regulation of cellular process	serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane
A [auth S], E [auth B]	Serine palmitoyltransferase 1	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	membrane lipid metabolic process sphingolipid metabolic process primary metabolic process metabolic process cellular process lipid metabolic process polyol metabolic process sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process lipid biosynthetic process alcohol metabolic process diol biosynthetic process sphingosine metabolic process membrane lipid metabolic process sphingolipid metabolic process primary metabolic process metabolic process cellular process lipid metabolic process polyol metabolic process sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process lipid biosynthetic 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 small molecule metabolic process membrane lipid biosynthetic process regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation regulation of programmed cell death cell death regulation of fat cell apoptotic process fat cell apoptotic process apoptotic process programmed cell death sphinganine metabolic process sphinganine biosynthetic process ceramide metabolic process amide biosynthetic process ceramide biosynthetic process amide metabolic process sphingomyelin biosynthetic process phospholipid biosynthetic process phospholipid metabolic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process sphingomyelin metabolic process positive regulation of autophagy catabolic process lipophagy macroautophagy autophagy positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of macroautophagy positive regulation of lipophagy regulation of lipophagy positive regulation of macroautophagy process utilizing autophagic mechanism regulation of metabolic process positive regulation of cellular 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E]	IPR051900	Serine palmitoyltransferase small subunit	Family
D [auth E]	IPR024512	Small subunit of serine palmitoyltransferase-like	Family
C [auth A]	IPR007203	ORMDL family	Family
B [auth T]	IPR001917	Aminotransferase, class-II, pyridoxal-phosphate binding site	Binding Site
B [auth T]	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
B [auth T]	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
B [auth T]	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
B [auth T]	IPR004839	Aminotransferase, class I/classII, large domain	Domain
B [auth T]	IPR050087	8-amino-7-oxononanoate synthase class-II	Family
A [auth S], E [auth B]	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A [auth S], E [auth B]	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A [auth S], E [auth B]	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A [auth S], E [auth B]	IPR004839	Aminotransferase, class I/classII, large domain	Domain
A [auth S], E [auth B]	IPR050087	8-amino-7-oxononanoate synthase class-II	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth E]	Pharos: Q969W0	adrenal cortex carcinoma glioblastoma invasive ductal breast carcinoma malignant colon neoplasm osteosarcoma psoriasis breast cancer hereditary spastic paraplegia lung adenocarcinoma malignant ependymoma ovarian cancer ductal breast carcinoma in situ interstitial lung disease lung cancer malignant glioma adrenal cortex carcinoma glioblastoma invasive ductal breast carcinoma malignant colon neoplasm osteosarcoma psoriasis breast cancer hereditary spastic paraplegia lung adenocarcinoma malignant ependymoma ovarian cancer ductal breast carcinoma in situ interstitial lung disease lung cancer malignant glioma pancreatic ductal adenocarcinoma
C [auth A]	Pharos: Q8N138	asthma ulcerative colitis acute lymphoblastic leukemia atrial fibrillation osteosarcoma systemic lupus erythematosus allergic rhinitis cervical cancer primary biliary cholangitis systemic sclerosis Crohn disease rheumatoid arthritis
B [auth T]	Pharos: O15270	neuropathy, hereditary sensory and autonomic, type 1C peripheral neuropathy pancreatic intraductal papillary-mucinous neoplasm Riley-Day syndrome atypical teratoid rhabdoid tumor glioblastoma intellectual disability malignant pancreatic neoplasm neurodegenerative disease osteosarcoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pilocytic astrocytoma subependymal giant cell astrocytoma Charcot-Marie-Tooth disease neuropathy, hereditary sensory and autonomic, type 1C peripheral neuropathy pancreatic intraductal papillary-mucinous neoplasm Riley-Day syndrome atypical teratoid rhabdoid tumor glioblastoma intellectual disability malignant pancreatic neoplasm neurodegenerative disease osteosarcoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pilocytic astrocytoma subependymal giant cell astrocytoma Charcot-Marie-Tooth disease hepatocellular carcinoma lung adenocarcinoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous carcinoma peripheral nervous system disease psoriasis tuberculosis cutaneous lupus erythematosus Hereditary Sensory Autonomic Neuropathy, Type 1 malignant glioma multiple sclerosis non-small cell lung carcinoma
A [auth S], E [auth B]	Pharos: O15269	neuropathy, hereditary sensory and autonomic, type 1A peripheral neuropathy Charcot-Marie-Tooth disease tuberculosis adenoma Emery-Dreifuss muscular dystrophy juvenile dermatomyositis myopathy ovarian cancer peripheral nervous system disease psoriasis astrocytic tumor Hereditary Sensory Autonomic Neuropathy, Type 1 large cell medulloblastoma neurodegenerative disease neuropathy, hereditary sensory and autonomic, type 1A peripheral neuropathy Charcot-Marie-Tooth disease tuberculosis adenoma Emery-Dreifuss muscular dystrophy juvenile dermatomyositis myopathy ovarian cancer peripheral nervous system disease psoriasis astrocytic tumor Hereditary Sensory Autonomic Neuropathy, Type 1 large cell medulloblastoma neurodegenerative disease Riley-Day syndrome intellectual disability pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma

Membrane Protein Annotation: OPM OPM Database Homepage

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

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth S], B [auth T], C [auth A], D [auth E], E [auth B]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	S-acyltransferases	Serine palmitoyltransferase (SPT) in complex with ORMDL3, dimer

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.