8EQU

Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A nanodisc

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: PDBTM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	SARS coronavirus Orf3/3a C-terminal domain	8093336	3002696	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SARS coronavirus viroporin transmembrane domain	8093337	3002697	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SARS coronavirus viroporin transmembrane domain	8093337	3002697	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SARS coronavirus Orf3/3a C-terminal domain	8093336	3002696	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	PF03489,PF05184	e8equC1	A: alpha arrays	X: Saposin-like	H: Saposin-like (From Topology)	T: Saposin-like	F: PF03489,PF05184	ECOD (1.6)
F	PF03489,PF05184	e8equF1	A: alpha arrays	X: Saposin-like	H: Saposin-like (From Topology)	T: Saposin-like	F: PF03489,PF05184	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF11289	Betacoronavirus viroporin (bCoV_viroporin)	Betacoronavirus viroporin	-	Family
C, F	PF05184	Saposin-like type B, region 1 (SapB_1)	Saposin-like type B, region 1	Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH sta ...	Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity [1,2]. It is one of the most studied members of the saposin protein family and it is involved in the hydrolysis of glycolipids and glycerolipids. SapB is unique in the saposin family in that it facilitates degradation by interacting with the substrate, not the enzymes [3].	Domain
C, F	PF03489	Saposin-like type B, region 2 (SapB_2)	Saposin-like type B, region 2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	ORF3a protein	molecular function activator activity molecular function regulator activity passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity identical protein binding protein binding binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis transmembrane transport localization transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis transmembrane transport localization transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport positive regulation of organelle organization regulation of cellular process macroautophagy autophagy regulation of reticulophagy modulation by virus of host process cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy positive regulation of reticulophagy cellular component disassembly positive regulation of autophagy regulation of biological process modulation by virus of host autophagy cellular metabolic process regulation of cellular metabolic process symbiont-mediated perturbation of host autophagy biological process involved in interaction with host regulation of organelle organization induction by virus of host reticulophagy regulation of macroautophagy metabolic process regulation of metabolic process symbiont-mediated perturbation of host cellular process catabolic process biological process involved in interspecies interaction between organisms positive regulation of cellular component organization regulation of cellular component organization positive regulation of biological process positive regulation of cellular metabolic process regulation of autophagy biological process involved in symbiotic interaction organelle disassembly viral process positive regulation of macroautophagy process utilizing autophagic mechanism modulation of process of another organism positive regulation of cellular process modulation by virus of host cellular process biological regulation regulation of catabolic process positive regulation of catabolic process organelle organization modulation by symbiont of host process reticulophagy regulation of cellular catabolic process positive regulation of cellular catabolic process	virion component virion membrane extracellular region cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host cell endoplasmic reticulum host intracellular region host cell cytoplasm part host intracellular organelle host cell lysosome virion component virion membrane extracellular region cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host cell endoplasmic reticulum host intracellular region host cell cytoplasm part host intracellular organelle host cell lysosome host cell endosome cell periphery plasma membrane membrane host cell membrane host cell endomembrane system host cell endoplasmic reticulum membrane protein-containing complex plasma membrane protein complex voltage-gated calcium channel complex membrane protein complex cation channel complex transporter complex transmembrane transporter complex calcium channel complex monoatomic ion channel complex host cell plasma membrane voltage-gated potassium channel complex potassium channel complex
C, F	Saposin-A	protein binding binding enzyme binding protease binding amide binding ceramide binding organic acid binding sphingolipid binding glycolipid binding ganglioside GM3 binding glycosphingolipid binding ion binding ganglioside binding anion binding protein binding binding enzyme binding protease binding amide binding ceramide binding organic acid binding sphingolipid binding glycolipid binding ganglioside GM3 binding glycosphingolipid binding ion binding ganglioside binding anion binding lipid binding carboxylic acid binding carbohydrate derivative binding monocarboxylic acid binding small molecule binding scaffold protein binding phospholipid binding ganglioside GM1 binding ganglioside GT1b binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein homodimerization activity protein dimerization activity ganglioside GM2 binding ganglioside GP1c binding	developmental process epithelial cell differentiation involved in prostate gland development multicellular organismal process epithelium development reproductive system development cellular developmental process prostate gland development reproductive process gland development animal organ development urogenital system development tissue development developmental process involved in reproduction epithelial cell differentiation multicellular organism development developmental process epithelial cell differentiation involved in prostate gland development multicellular organismal process epithelium development reproductive system development cellular developmental process prostate gland development reproductive process gland development animal organ development urogenital system development tissue development developmental process involved in reproduction epithelial cell differentiation multicellular organism development cell differentiation anatomical structure development reproductive structure development cellular process system development regulation of biological process organic substance metabolic process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process regulation of metabolic process lipid metabolic process regulation of primary metabolic process membrane lipid metabolic process organonitrogen compound metabolic process cellular metabolic process cellular lipid metabolic process sphingolipid metabolic process cellular localization organic anion transport nitrogen compound transport carboxylic acid transport transport glycolipid transport organic substance transport lipid localization lipid transport localization within membrane carbohydrate derivative transport establishment of localization organic acid transport localization ceramide transport amide transport macromolecule localization ganglioside GM1 transport to membrane establishment of localization in cell vacuolar transport intracellular transport lysosomal transport cellular response to stimulus regulation of cellular process response to stimulus signaling cell communication adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of beta-galactosidase activity positive regulation of catalytic activity catabolic process autophagy regulation of cellular metabolic process regulation of catabolic process regulation of autophagy cellular catabolic process regulation of cellular catabolic process process utilizing autophagic mechanism developmental growth growth organ growth prostate gland growth	membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole cellular anatomical entity intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole cellular anatomical entity intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix intracellular vesicle endomembrane system bounding membrane of organelle vesicle membrane cytoplasmic vesicle vacuolar membrane membrane azurophil granule lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane organelle membrane secretory granule membrane plasma membrane endosome late endosome
D, E, G, H	Saposin A, polyalanine model	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR046446	3a-like viroporin, cytosolic domain, alpha/betacoronavirus	Domain
A, B	IPR024407	Protein 3a, betacoronavirus	Family
A, B	IPR046445	3a-like viroporin, transmembrane domain, alpha/betacoronavirus	Domain
C, F	IPR011001	Saposin-like	Homologous Superfamily
C, F	IPR008373	Saposin	Family
C, F	IPR007856	Saposin-like type B, region 1	Domain
C, F	IPR021165	Saposin, chordata	Family
C, F	IPR003119	Saposin A-type domain	Domain
C, F	IPR008139	Saposin B type domain	Domain
C, F	IPR008138	Saposin B type, region 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F	Pharos: P07602	Krabbe disease, atypical, due to saposin A deficiency atypical Gaucher disease due to saposin C deficiency encephalopathy due to prosaposin deficiency metachromatic leukodystrophy due to saposin b deficiency metachromatic leukodystrophy leukodystrophy gangliosidosis Gaucher disease myopathy Parkinson disease sphingolipidosis astrocytic tumor brain disease inborn errors of metabolism Metachromatic Leukodystrophy, Infant Krabbe disease, atypical, due to saposin A deficiency atypical Gaucher disease due to saposin C deficiency encephalopathy due to prosaposin deficiency metachromatic leukodystrophy due to saposin b deficiency metachromatic leukodystrophy leukodystrophy gangliosidosis Gaucher disease myopathy Parkinson disease sphingolipidosis astrocytic tumor brain disease inborn errors of metabolism Metachromatic Leukodystrophy, Infant neurodegenerative disease plasma cell myeloma ovarian cancer psoriasis B-cell chronic lymphocytic leukemia IgA glomerulonephritis intellectual disability lysosomal storage disease

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

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 R01GM133198.