1F8V | pdb_00001f8v

THE STRUCTURE OF PARIACOTO VIRUS REVEALS A DODECAHEDRAL CAGE OF DUPLEX RNA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
G [auth F]	d1f8v.3	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	Nodaviridae-like VP	Alphanodavirus capsid protein	(Pariacoto virus ) [TaxId: 103782 ],	SCOPe (2.08)
E	d1f8v.2	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	Nodaviridae-like VP	Alphanodavirus capsid protein	(Pariacoto virus ) [TaxId: 103782 ],	SCOPe (2.08)
C [auth D]	d1f8v.1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	Nodaviridae-like VP	Alphanodavirus capsid protein	(Pariacoto virus ) [TaxId: 103782 ],	SCOPe (2.08)
F [auth C]	d1f8v.3	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	Nodaviridae-like VP	Alphanodavirus capsid protein	(Pariacoto virus ) [TaxId: 103782 ],	SCOPe (2.08)
D [auth B]	d1f8v.2	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	Nodaviridae-like VP	Alphanodavirus capsid protein	(Pariacoto virus ) [TaxId: 103782 ],	SCOPe (2.08)
B [auth A]	d1f8v.1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	Nodaviridae-like VP	Alphanodavirus capsid protein	(Pariacoto virus ) [TaxId: 103782 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth C]	SCOP2 Family	Nodaviridae-like VP	8071985	4003472	SCOP2 (2022-06-29)
F [auth C]	SCOP2 Superfamily	Positive stranded ssRNA viruses-like	8071986	3000918	SCOP2 (2022-06-29)
D [auth B]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8071986	3000918	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8071986	3000918	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)
B [auth A]	Rhv	e1f8vA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: Rhv	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth C]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D [auth B]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B [auth A]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], E, G [auth F]	MATURE CAPSID PROTEIN GAMMA	aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity cation binding ion binding binding metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont entry into host cell via permeabilization of host membrane viral life cycle symbiont-mediated disruption of host cellular anatomical structure biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host membrane proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont entry into host cell via permeabilization of host membrane viral life cycle symbiont-mediated disruption of host cellular anatomical structure biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host membrane symbiont entry into host cell viral process symbiont entry into host disruption of anatomical structure in another organism	viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component
B [auth A], D [auth B], F [auth C]	MATURE CAPSID PROTEIN BETA	aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity cation binding ion binding binding metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont entry into host cell via permeabilization of host membrane viral life cycle symbiont-mediated disruption of host cellular anatomical structure biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host membrane proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont entry into host cell via permeabilization of host membrane viral life cycle symbiont-mediated disruption of host cellular anatomical structure biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host membrane symbiont entry into host cell viral process symbiont entry into host disruption of anatomical structure in another organism	viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component
A [auth R]	RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], E, G [auth F]	IPR029053	Viral coat protein subunit	Homologous Superfamily
C [auth D], E, G [auth F]	IPR000696	Peptidase A6, nodavirus coat protein	Family
B [auth A], D [auth B], F [auth C]	IPR029053	Viral coat protein subunit	Homologous Superfamily
B [auth A], D [auth B], F [auth C]	IPR000696	Peptidase A6, nodavirus coat protein	Family

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.