3D0I | pdb_00003d0i

Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth F]	d3d0if_	Alpha and beta proteins (a+b)	SARS receptor-binding domain-like	SARS receptor-binding domain-like	SARS receptor-binding domain-like	Spike protein S1	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)
C [auth E]	d3d0ie_	Alpha and beta proteins (a+b)	SARS receptor-binding domain-like	SARS receptor-binding domain-like	SARS receptor-binding domain-like	Spike protein S1	SARS-CoV (Severe acute respiratory syndrome-related coronavirus ) [TaxId: 694009 ],	SCOPe (2.08)
B	d3d0ib_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Neurolysin-like	Angiotensin converting enzyme 2, ACE2	Masked palm civet (Paguma larvata ) [TaxId: 9675 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3d0ia_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Neurolysin-like	Angiotensin converting enzyme 2, ACE2	Masked palm civet (Paguma larvata ) [TaxId: 9675 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth F]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8041894	3001706	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8041894	3001706	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8037105	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8037105	3001975	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 [auth F]	RasGEF	e3d0iF1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: RasGEF	ECOD (v294.2)
C [auth E]	RasGEF	e3d0iE1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: RasGEF	ECOD (v294.2)
B	RasGEF	e3d0iB1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: RasGEF	ECOD (v294.2)
A	RasGEF	e3d0iA1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: RasGEF	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth F]	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (4.3.0)
C [auth E]	3.30.70.1840	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Spike protein, C-terminal core receptor binding subdomain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth E], D [auth F]	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
A, B	PF01401	Angiotensin-converting enzyme (Peptidase_M2)	Angiotensin-converting enzyme	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E], D [auth F]	Spike glycoprotein	host cell surface binding binding host cell surface receptor binding 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 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 viral life cycle adhesion of symbiont to 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 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 viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction 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 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	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part 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 cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part 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
A, B	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 cation binding ion 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 cation binding ion binding metal ion binding small molecule binding metallocarboxypeptidase activity metalloexopeptidase activity endopeptidase activity identical protein binding transporter activator activity molecular function activator activity molecular function regulator activity transporter regulator activity transition metal ion binding zinc ion binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process 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 proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process 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 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 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 regulation of macromolecule biosynthetic 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 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	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 extracellular exosome extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane organelle membrane endocytic vesicle membrane-enclosed lumen endomembrane system intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum 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
C [auth E], D [auth F]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
C [auth E], D [auth F]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
C [auth E], D [auth F]	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
C [auth E], D [auth F]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
C [auth E], D [auth F]	IPR042578	Spike glycoprotein, betacoronavirus	Family
C [auth E], D [auth F]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
C [auth E], D [auth F]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
C [auth E], D [auth F]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
C [auth E], D [auth F]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
C [auth E], D [auth F]	IPR002552	Spike glycoprotein S2, coronavirus	Domain
C [auth E], D [auth F]	IPR044370	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV	Domain
A, B	IPR031588	Collectrin domain	Domain
A, B	IPR001548	Peptidase M2, peptidyl-dipeptidase A	Family
A, B	IPR031588	Collectrin domain	Domain
A, B	IPR001548	Peptidase M2, peptidyl-dipeptidase A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	: 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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URL: https://www.rcsb.org/annotations/3D0I

⇱ Annotations: 3D0I