8Y6A

Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD in complex with human ACE2 and S309 Fab

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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	8037105	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C	Heavy Chain	IGHV1	-	spike protein s1	SAbDab (2025-03-07)
D	Light Chain	IGKV3	Kappa	spike protein s1	SAbDab (2025-03-07)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
C	Beludavimab	SARS-CoV-2 Spike RBD	Therapeutic SAbDab (2025-03-07)
D	Beludavimab	SARS-CoV-2 Spike RBD	Therapeutic SAbDab (2025-03-07)

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 translat ...	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	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 transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding	regulation of systemic arterial blood pressure by renin-angiotensin regulation of systemic arterial blood pressure by hormone multicellular organismal process peptide hormone processing regulation of systemic arterial blood pressure mediated by a chemical signal system process signaling receptor ligand precursor processing protein maturation circulatory system process proteolysis amide metabolic process protein metabolic process regulation of biological quality blood circulation regulation of systemic arterial blood pressure by renin-angiotensin regulation of systemic arterial blood pressure by hormone multicellular organismal process peptide hormone processing regulation of systemic arterial blood pressure mediated by a chemical signal system process signaling receptor ligand precursor processing protein maturation circulatory system process proteolysis amide metabolic process protein metabolic process regulation of biological quality blood circulation regulation of blood pressure regulation of hormone levels biological regulation regulation of systemic arterial blood pressure by circulatory renin-angiotensin primary metabolic process gene expression macromolecule biosynthetic process hormone metabolic process regulation of systemic arterial blood pressure endocrine process biosynthetic process regulation of angiotensin levels in blood protein processing metabolic process cellular process macromolecule metabolic process angiotensin maturation membrane organization cellular component organization membrane fusion cellular component organization or biogenesis heart process regulation of biological process regulation of cardiac conduction regulation of heart contraction regulation of system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process heart contraction regulation of blood volume by renin-angiotensin nervous system process feeding behavior brain renin-angiotensin system behavior drinking behavior angiotensin-mediated drinking behavior nervous system process involved in regulation of systemic arterial blood pressure viral process viral life cycle regulation of cellular process positive regulation of cellular component organization regulation of cellular component organization gap junction assembly positive regulation of biological process cellular component biogenesis cellular component assembly positive regulation of gap junction assembly cell junction assembly 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 regulation of localization regulation of transport transport regulation of transmembrane transporter activity establishment of localization regulation of transporter activity transmembrane transport regulation of molecular function localization regulation of transmembrane transport import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms biological process involved in interaction with host vesicle-mediated transport biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell receptor-mediated endocytosis endocytosis 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 regulation of tube diameter regulation of tube size regulation of vasoconstriction vascular process in circulatory system blood vessel diameter maintenance vasoconstriction regulation of anatomical structure size 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 regulation of signaling receptor activity negative regulation of molecular function negative regulation of signaling receptor activity regulation of biosynthetic process regulation of macromolecule metabolic process regulation of gene expression regulation of cytokine production cytokine production regulation of macromolecule biosynthetic process regulation of metabolic process reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process positive regulation of metabolic process regulation of reactive oxygen species metabolic process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host regulation of defense response regulation of response to external stimulus defense response regulation of inflammatory response response to external stimulus response to stress regulation of response to stress inflammatory response nitrogen compound transport positive regulation of amine transport amine transport amino acid transport positive regulation of amino acid transport positive regulation of transport regulation of amino acid transport regulation of amine transport aromatic amino acid transport organic anion transport carboxylic acid transport organic cation transport organic acid transport tryptophan transport carboxylic acid transmembrane transport regulation of L-proline import across plasma membrane regulation of proline transport organic acid transmembrane transport import across plasma membrane L-proline transmembrane transport proline transport regulation of amino acid import across plasma membrane L-alpha-amino acid transmembrane transport amino acid import across plasma membrane proline import across plasma membrane 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 neutral amino acid transport L-proline import across plasma membrane positive regulation of organic acid transport proline transmembrane transport positive regulation of proline import across plasma membrane regulation of organic acid transport entry receptor-mediated virion attachment to host cell 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 membrane cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane extracellular exosome extracellular vesicle membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection membrane cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cell surface membrane microdomain membrane raft intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane cytoplasm organelle membrane endocytic vesicle membrane-enclosed lumen endomembrane system intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum brush border membrane cluster of actin-based cell projections brush border cell projection membrane
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 symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated-mediated suppression of host tetherin activity modulation of process of another organism biological process involved in interaction with host 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 symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated-mediated suppression of host tetherin activity modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host viral gene expression viral translation fusion of virus membrane with host plasma membrane symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell 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 symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response 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
C	heavy chain of S309 Fab	-	-	-
D	light chain of S309 Fab	-	-	-

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9BYF1	endomyocardial fibrosis hypertensive disorder abdominal aortic aneurysm inborn carbohydrate metabolic disorder kidney disease Middle East respiratory syndrome obesity disorder pulmonary edema adult acute respiratory distress syndrome Spontaneous abortion common cold ulcerative colitis COVID-19–associated multisystem inflammatory syndrome in children cystic fibrosis heart disease endomyocardial fibrosis hypertensive disorder abdominal aortic aneurysm inborn carbohydrate metabolic disorder kidney disease Middle East respiratory syndrome obesity disorder pulmonary edema adult acute respiratory distress syndrome Spontaneous abortion common cold ulcerative colitis COVID-19–associated multisystem inflammatory syndrome in children cystic fibrosis heart disease influenza nephrosclerosis pneumonia pulmonary embolism cerebrovascular disorder thrombotic disease coronary artery disease Crohn disease diabetes mellitus diarrheal disease Ebola hemorrhagic fever intellectual disability lymphopenia psoriasis severe acute respiratory syndrome chronic obstructive pulmonary disease transitional cell carcinoma COVID-19 cutaneous lupus erythematosus diabetic kidney disease disseminated intravascular coagulation

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.