7YVU

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8104349	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01401	Angiotensin-converting enzyme (Peptidase_M2)	Angiotensin-converting enzyme	-	Family
B	PF09408	Betacoronavirus spike glycoprotein S1, receptor binding (bCoV_S1_RBD)	Betacoronavirus spike glycoprotein S1, receptor binding	This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is transla ...	This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion [1]. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilise both the S1 NTD and S1 RBD for viral entry [2]. SARS-CoV makes use of its S1 RBD to bind to the human angiotensin-converting enzyme 2 (ACE2) as its host receptor [3,4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Processed angiotensin-converting enzyme 2	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity protein binding binding virus receptor activity exogenous protein binding peptidyl-dipeptidase activity exopeptidase activity carboxypeptidase activity endopeptidase activity cation binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity protein binding binding virus receptor activity exogenous protein binding peptidyl-dipeptidase activity exopeptidase activity carboxypeptidase activity endopeptidase activity cation binding ion binding metal ion binding small molecule binding identical protein binding	heart process multicellular organismal process system process regulation of biological process regulation of cardiac conduction regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process heart contraction blood circulation heart process multicellular organismal process system process regulation of biological process regulation of cardiac conduction regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process heart contraction blood circulation regulation of systemic arterial blood pressure by renin-angiotensin regulation of systemic arterial blood pressure by hormone regulation of blood volume by renin-angiotensin regulation of systemic arterial blood pressure mediated by a chemical signal nervous system process regulation of blood pressure feeding behavior brain renin-angiotensin system behavior regulation of systemic arterial blood pressure endocrine process drinking behavior angiotensin-mediated drinking behavior regulation of biological quality nervous system process involved in regulation of systemic arterial blood pressure positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization gap junction assembly positive regulation of biological process cellular component organization cellular component biogenesis cellular component assembly positive regulation of gap junction assembly cell junction assembly cellular component organization or biogenesis positive regulation of cellular process cell-cell junction assembly cell-cell junction organization positive regulation of cellular component biogenesis regulation of gap junction assembly regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly cell junction organization cellular process multi-multicellular organism process maternal process involved in female pregnancy reproductive process multicellular organismal reproductive process female pregnancy multi-organism reproductive process negative regulation of cell population proliferation cell population proliferation regulation of smooth muscle cell proliferation negative regulation of biological process smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation regulation of cell population proliferation negative regulation of cellular process muscle cell proliferation cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade aromatic amino acid transport nitrogen compound transport organic anion transport carboxylic acid transport transport establishment of localization organic cation transport organic acid transport amino acid transport localization tryptophan transport proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process regulation of localization carboxylic acid transmembrane transport regulation of L-proline import across plasma membrane positive regulation of amine transport regulation of amino acid transport regulation of proline transport organic acid transmembrane transport import across plasma membrane L-proline transmembrane transport proline transport transmembrane transport regulation of amino acid import across plasma membrane regulation of transmembrane transport positive regulation of amino acid transport L-alpha-amino acid transmembrane transport amino acid import across plasma membrane proline import across plasma membrane import into cell regulation of proline import across plasma membrane positive regulation of L-proline import across plasma membrane amino acid transmembrane transport L-amino acid transport positive regulation of transmembrane transport regulation of amino acid transmembrane transport regulation of transport neutral amino acid transport L-proline import across plasma membrane positive regulation of organic acid transport amine transport proline transmembrane transport positive regulation of transport positive regulation of proline import across plasma membrane regulation of organic acid transport regulation of amine transport virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction positive regulation of blood circulation positive regulation of cardiac muscle contraction cardiac muscle contraction striated muscle contraction positive regulation of striated muscle contraction regulation of cardiac muscle contraction muscle contraction muscle system process regulation of muscle system process positive regulation of heart contraction regulation of striated muscle contraction regulation of muscle contraction positive regulation of muscle contraction positive regulation of multicellular organismal process	membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane cell surface intracellular anatomical structure membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane cell surface intracellular anatomical structure cytoplasm brush border membrane cluster of actin-based cell projections brush border cell projection membrane extracellular region extracellular space
B	Spike protein S1	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity host cell surface binding host cell surface receptor binding structural constituent of virion structural molecule activity identical protein binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization biological process involved in interaction with host vesicle-mediated transport biological process involved in symbiotic interaction localization symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell endocytosis receptor-mediated endocytosis transport of virus symbiont-mediated perturbation of host defense response suppression by virus of host tetherin activity modulation by virus of host process virus-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation of process of another organism modulation by virus of host cellular process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host viral gene expression viral translation fusion of virus membrane with host plasma membrane regulation of biological process positive regulation of viral life cycle positive regulation of viral process biological regulation positive regulation of biological process modulation by symbiont of entry into host regulation of viral entry into host cell regulation of viral life cycle regulation of viral process positive regulation of viral entry into host cell positive regulation by symbiont of entry into host regulation of biological process involved in symbiotic interaction response to host defenses response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus entry receptor-mediated virion attachment to host cell	cellular anatomical structure membrane host extracellular space host cellular component cell periphery plasma membrane host intracellular membrane-bounded organelle host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm cellular anatomical structure membrane host extracellular space host cellular component cell periphery plasma membrane host intracellular membrane-bounded organelle host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region host cell plasma membrane virion component virion membrane viral membrane viral envelope host cell surface

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR031588	Collectrin domain	Domain
A	IPR001548	Peptidase M2, peptidyl-dipeptidase A	Family
B	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
B	IPR044366	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2	Domain
B	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
B	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
B	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
B	IPR042578	Spike glycoprotein, betacoronavirus	Family
B	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
B	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
B	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
B	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
B	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
B	IPR002552	Spike glycoprotein S2, coronavirus	Domain

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.