Annotations: 9XI4

SARS-CoV-2 Omicron BA.4/5 spike RBD in complex with BD56-104 Fab and ACE2

External Resource: Annotation

Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth L]	Light chain of BD56-104 Fab	-	-	-
C [auth H]	Heavy chain of BD56-104 Fab	-	-	-
B [auth E]	Spike protein S1	molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity host cell surface binding binding host cell surface receptor binding structural constituent of virion structural molecule activity identical protein binding 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 disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host tissue disruption of anatomical structure in another organism symbiont entry into host cell symbiont entry into 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 disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host tissue disruption of anatomical structure in another organism symbiont entry into host cell symbiont entry into host viral life cycle 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 adhesion of symbiont to host fusion of virus membrane with host plasma membrane endocytosis involved in viral entry into host cell symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process symbiont-mediated-mediated suppression of host tetherin activity modulation of process of another organism 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 cellular component host extracellular region other organism part 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 cellular anatomical structure membrane host cellular component host extracellular region other organism part 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
A	Processed angiotensin-converting enzyme 2	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity metallocarboxypeptidase activity exopeptidase activity metalloexopeptidase activity carboxypeptidase activity endopeptidase activity identical protein binding protein binding binding virus receptor activity peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity metallocarboxypeptidase activity exopeptidase activity metalloexopeptidase activity carboxypeptidase activity endopeptidase activity identical protein binding protein binding binding virus receptor activity exogenous protein binding peptidyl-dipeptidase activity transporter activator activity molecular function activator activity molecular function regulator activity transporter regulator activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 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 organization 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 biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction 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 negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process 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 virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host transmembrane transport amino acid transport localization import into cell transport import across plasma membrane amino acid import across plasma membrane amino acid transmembrane transport establishment of localization RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process organic acid transport aromatic amino acid transport nitrogen compound transport carboxylic acid transport tryptophan transport 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 peptide hormone processing signaling receptor ligand precursor processing protein maturation proteolysis protein metabolic process regulation of hormone levels regulation of systemic arterial blood pressure by circulatory renin-angiotensin hormone metabolic process regulation of angiotensin levels in blood protein processing angiotensin maturation membrane organization membrane fusion receptor-mediated endocytosis of virus by host cell vesicle-mediated transport 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 smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation regulation of cytokine production cytokine production 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 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 regulation of localization regulation of transport positive regulation of amine transport amine transport positive regulation of amino acid transport positive regulation of transport regulation of amino acid transport regulation of amine transport proline import across plasma membrane carboxylic acid transmembrane transport regulation of L-proline import across plasma membrane regulation of proline import across plasma membrane positive regulation of L-proline import across plasma membrane L-amino acid transport positive regulation of transmembrane transport regulation of proline transport regulation of amino acid transmembrane transport L-proline transmembrane transport neutral amino acid transport proline transport L-proline import across plasma membrane positive regulation of organic acid transport regulation of amino acid import across plasma membrane regulation of transmembrane transport proline transmembrane transport positive regulation of proline import across plasma membrane regulation of organic acid transport L-alpha-amino acid transmembrane transport entry receptor-mediated virion attachment to host cell	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle 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 cell projection cilium plasma membrane bounded cell projection cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane cell surface membrane microdomain membrane raft brush border membrane cluster of actin-based cell projections brush border cell projection membrane

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

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

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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.

9XI4 | pdb_00009xi4

SARS-CoV-2 Omicron BA.4/5 spike RBD in complex with BD56-104 Fab and ACE2

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation