Annotations: 7KJR

Cryo-EM structure of SARS-CoV-2 ORF3a

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	SARS coronavirus viroporin, transmembrane domain	8093337	3002697	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SARS coronavirus Orf3/3a, C-terminal domain	8093336	3002696	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)
D	MIF4G	e7kjrD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
C	Viral_Rep	e7kjrC01	A: beta barrels	X: Histone-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F: Viral_Rep	ECOD (v294.2)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Apolipoprotein A-I	amyloid-beta binding binding peptide binding high-density lipoprotein particle receptor binding protein binding signaling receptor binding lipoprotein particle receptor binding heat shock protein binding phospholipid binding lipid binding sterol transfer activity lipid carrier activity lipid transfer activity transporter activity amyloid-beta binding binding peptide binding high-density lipoprotein particle receptor binding protein binding signaling receptor binding lipoprotein particle receptor binding heat shock protein binding phospholipid binding lipid binding sterol transfer activity lipid carrier activity lipid transfer activity transporter activity cholesterol transfer activity molecular carrier activity apolipoprotein A-I receptor binding apolipoprotein receptor binding lipoprotein particle binding protein-containing complex binding protein-lipid complex binding high-density lipoprotein particle binding identical protein binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity phosphatidylcholine-sterol O-acyltransferase activator activity sterol binding alcohol binding steroid binding cholesterol binding small molecule binding signaling receptor regulator activity receptor ligand activity signaling receptor activator activity protein homodimerization activity protein dimerization activity chemorepellent activity enzyme binding	positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process regulation of transport biological regulation lipid localization lipid transport positive regulation of lipid localization establishment of localization positive regulation of lipid transport positive regulation of transport regulation of lipid localization macromolecule localization cholesterol transport cholesterol efflux vitamin transport regulation of protein stability regulation of biological quality protein stabilization phospholipid homeostasis chemical homeostasis homeostatic process lipid homeostasis reverse cholesterol transport triglyceride homeostasis acylglycerol homeostasis endothelial cell migration blood vessel endothelial cell migration cell migration cellular process cell motility import into cell positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization vesicle-mediated transport cellular component organization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis endocytosis multicellular organismal process regulation of immune effector process response to stimulus negative regulation of biological process cytokine production negative regulation of cellular process regulation of cytokine production regulation of immune system process regulation of multicellular organismal process cytokine production involved in immune response negative regulation of macromolecule metabolic process production of molecular mediator of immune response regulation of biosynthetic process negative regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response immune response negative regulation of metabolic process negative regulation of immune effector process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of gene expression negative regulation of production of molecular mediator of immune response negative regulation of gene expression biosynthetic process negative regulation of immune system process negative regulation of biosynthetic process immune system process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response negative regulation of multicellular organismal process regulation of metabolic process positive regulation of substrate adhesion-dependent cell spreading regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion substrate adhesion-dependent cell spreading embryo development negative regulation of cell adhesion regulation of cell-cell adhesion involved in gastrulation heterotypic cell-cell adhesion multicellular organism development cell-cell adhesion anatomical structure development regulation of cell-cell adhesion regulation of heterotypic cell-cell adhesion developmental process cell-cell adhesion involved in gastrulation embryonic morphogenesis gastrulation anatomical structure morphogenesis negative regulation of heterotypic cell-cell adhesion negative regulation of cell-cell adhesion chemotaxis negative chemotaxis taxis response to chemical response to external stimulus locomotion protein-containing complex remodeling protein-lipid complex organization very-low-density lipoprotein particle remodeling protein-lipid complex remodeling negative regulation of very-low-density lipoprotein particle remodeling plasma lipoprotein particle organization negative regulation of cellular component organization protein-containing complex organization plasma lipoprotein particle remodeling regulation of plasma lipoprotein particle levels regulation of very-low-density lipoprotein particle remodeling triglyceride-rich lipoprotein particle remodeling peptidyl-methionine modification macromolecule modification peptidyl-amino acid modification primary metabolic process protein metabolic process protein modification process system process regulation of intestinal absorption digestive system process regulation of system process lipid digestion regulation of digestive system process intestinal lipid absorption digestion intestinal absorption regulation of intestinal lipid absorption intestinal cholesterol absorption regulation of intestinal cholesterol absorption protein oxidation cholesterol import cell population proliferation endothelial cell proliferation epithelial cell proliferation lipoprotein biosynthetic process lipoprotein metabolic process cellular component biogenesis cellular component assembly high-density lipoprotein particle assembly protein-containing complex assembly plasma lipoprotein particle assembly protein-lipid complex assembly glycerophospholipid biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid biosynthetic process phospholipid metabolic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphatidylcholine metabolic process glycerolipid metabolic process phosphatidylcholine biosynthetic process phosphorus metabolic process lipid metabolic process glucocorticoid metabolic process steroid metabolic process phospholipid transport organophosphate ester transport phospholipid efflux cellular response to stimulus regulation of signaling small GTPase-mediated signal transduction signaling regulation of small GTPase mediated signal transduction regulation of signal transduction regulation of Cdc42 protein signal transduction regulation of Rho protein signal transduction intracellular signal transduction Rho protein signal transduction Cdc42 protein signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication signal transduction integrin-mediated signaling pathway cell surface receptor signaling pathway regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus regulation of inflammatory response response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response interleukin-1 production regulation of interleukin-1 beta production negative regulation of interleukin-1 beta production negative regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of intracellular signal transduction positive regulation of Rho protein signal transduction positive regulation of small GTPase mediated signal transduction positive regulation of signaling regulation of cholesterol metabolic process regulation of lipid metabolic process sterol metabolic process cholesterol metabolic process alcohol metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of lipid metabolic process small molecule metabolic process regulation of steroid metabolic process secondary alcohol metabolic process positive regulation of cholesterol metabolic process positive regulation of steroid metabolic process positive regulation of small molecule metabolic process sterol homeostasis cholesterol homeostasis secondary alcohol biosynthetic process small molecule biosynthetic process cholesterol biosynthetic process sterol biosynthetic process alcohol biosynthetic process steroid biosynthetic process regulation of cell adhesion molecule production negative regulation of cell adhesion molecule production cell adhesion molecule production amyloid precursor protein catabolic process amyloid-beta metabolic process amyloid precursor protein metabolic process amyloid-beta formation high-density lipoprotein particle clearance plasma lipoprotein particle clearance adrenal gland development endocrine system development gland development animal organ development system development high-density lipoprotein particle remodeling lipid storage nutrient storage response to cytokine response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus cellular response to lipoprotein particle stimulus G protein-coupled receptor signaling pathway regulation of phospholipid transport positive regulation of phospholipid efflux regulation of phospholipid efflux positive regulation of phospholipid transport negative regulation of signaling negative regulation of cell communication cytokine-mediated signaling pathway cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway negative regulation of tumor necrosis factor-mediated signaling pathway negative regulation of signal transduction negative regulation of cytokine-mediated signaling pathway response to tumor necrosis factor positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly actin filament-based process stress fiber assembly regulation of actin filament organization actin cytoskeleton organization actomyosin structure organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization actin filament organization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of organelle organization regulation of stress fiber assembly organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization	protein-containing complex cellular anatomical structure extracellular region plasma lipoprotein particle high-density lipoprotein particle extracellular protein-containing complex lipoprotein particle protein-lipid complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle protein-containing complex cellular anatomical structure extracellular region plasma lipoprotein particle high-density lipoprotein particle extracellular protein-containing complex lipoprotein particle protein-lipid complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle endocytic vesicle membrane-enclosed lumen endomembrane system intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum spherical high-density lipoprotein particle cell periphery plasma membrane membrane early endosome endosome blood microparticle chylomicron low-density lipoprotein particle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen secretory granule secretory vesicle endocytic vesicle lumen very-low-density lipoprotein particle triglyceride-rich plasma lipoprotein particle
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	symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated activation of host reticulophagy symbiont-mediated perturbation of host autophagy modulation of process of another organism symbiont-mediated activation of host autophagy biological process involved in interaction with host biological process involved in symbiotic interaction	virion component virion membrane cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host intracellular region virion component virion membrane cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host intracellular region 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 cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane voltage-gated potassium channel complex potassium channel complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR050163	Apolipoprotein A1/A4/E	Family
C, D	IPR000074	Apolipoprotein A/E	Family
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	: P02647	familial visceral amyloidosis hypertensive disorder membranous glomerulonephritis coronary artery disease Behcet disease Hypoxia acute lung injury amyloidosis HIV infectious disease peripheral neuropathy cerebrovascular disorder Tangier disease hypoalphalipoproteinemia, primary, 1 inherited lipid metabolism disorder adenocarcinoma familial visceral amyloidosis hypertensive disorder membranous glomerulonephritis coronary artery disease Behcet disease Hypoxia acute lung injury amyloidosis HIV infectious disease peripheral neuropathy cerebrovascular disorder Tangier disease hypoalphalipoproteinemia, primary, 1 inherited lipid metabolism disorder adenocarcinoma granular cell carcinoma hypoalphalipoproteinemia tubular adenocarcinoma malignant mesothelioma atherosclerosis psoriasis type 2 diabetes mellitus abdominal aortic aneurysm drug-induced liver injury lung benign neoplasm familial isolated deficiency of vitamin E gastric neoplasm metabolic disease non-alcoholic fatty liver disease hereditary diffuse gastric adenocarcinoma hypertrophic pyloric stenosis cribriform carcinoma idiopathic membranous glomerulonephritis acquired metabolic disease metabolic syndrome X obesity disorder periodic fever syndrome cribriform carcinoma of breast inborn carbohydrate metabolic disorder lung adenocarcinoma gastric cancer heart disease hepatocellular carcinoma ovarian cancer apolipoprotein A-I deficiency peripheral nervous system disease

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Transmembrane	Alpha-helical polytopic	Polytopic viroporins	Betacoronavirus viroporin 3a

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

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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.