9EAC | pdb_00009eac

Seneca valley virus Empty rotated particle at acidic condition (ER-particle[C])

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)
B	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8068058	3000918	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22663	Picornavirus coat protein (Rhv_5)	Picornavirus coat protein	This domain is found in capsid proteins from picornavirus, such as enterovirus, rhinovirus and foot-and-mouth disease virus [1-5].	Domain
B	PF00073	picornavirus capsid protein (Rhv)	picornavirus capsid protein	CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised. The family should probably be split up into sub-families. Capsid proteins of picornavi ...	CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.	Domain
C	PF00073	picornavirus capsid protein (Rhv)	picornavirus capsid protein	CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised. The family should probably be split up into sub-families. Capsid proteins of picornavi ...	CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Capsid protein VP1	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides ATP-dependent activity passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity structural molecule activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response biological process involved in interaction with host symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host innate immune response symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity symbiont entry into host cell symbiont entry into host symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated suppression of host TRAF-mediated signal transduction transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell gene expression DNA-templated transcription symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity proteolysis protein metabolic process entry receptor-mediated virion attachment to host cell	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell nucleus other organism part host cell nucleolus host cell nuclear part host intracellular organelle cellular anatomical structure host cell part host intracellular region membrane host cell membrane host cell cytoplasmic vesicle membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell nucleus other organism part host cell nucleolus host cell nuclear part host intracellular organelle cellular anatomical structure host cell part host intracellular region membrane host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host cell cytoplasmic vesicle host cell cytoplasm viral capsid icosahedral viral capsid virion component T=pseudo3 icosahedral viral capsid
B	Capsid protein VP3	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides ATP-dependent activity passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity structural molecule activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response biological process involved in interaction with host symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host innate immune response symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity symbiont entry into host cell symbiont entry into host symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated suppression of host TRAF-mediated signal transduction transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell gene expression DNA-templated transcription symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity proteolysis protein metabolic process entry receptor-mediated virion attachment to host cell	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell nucleus other organism part host cell nucleolus host cell nuclear part host intracellular organelle cellular anatomical structure host cell part host intracellular region membrane host cell membrane host cell cytoplasmic vesicle membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell nucleus other organism part host cell nucleolus host cell nuclear part host intracellular organelle cellular anatomical structure host cell part host intracellular region membrane host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host cell cytoplasmic vesicle host cell cytoplasm viral capsid icosahedral viral capsid virion component T=pseudo3 icosahedral viral capsid
C	Capsid protein VP2	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides ATP-dependent activity passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity structural molecule activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response biological process involved in interaction with host symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host innate immune response symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity symbiont entry into host cell symbiont entry into host symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated suppression of host TRAF-mediated signal transduction transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell gene expression DNA-templated transcription symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity proteolysis protein metabolic process entry receptor-mediated virion attachment to host cell	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell nucleus other organism part host cell nucleolus host cell nuclear part host intracellular organelle cellular anatomical structure host cell part host intracellular region membrane host cell membrane host cell cytoplasmic vesicle membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell nucleus other organism part host cell nucleolus host cell nuclear part host intracellular organelle cellular anatomical structure host cell part host intracellular region membrane host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host cell cytoplasmic vesicle host cell cytoplasm viral capsid icosahedral viral capsid virion component T=pseudo3 icosahedral viral capsid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A	IPR000199	Peptidase C3A/C3B, picornaviral	Domain
A	IPR001676	Picornavirus capsid	Domain
A	IPR014759	Helicase, superfamily 3, single-stranded RNA virus	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR029053	Viral coat protein subunit	Homologous Superfamily
A	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A	IPR004004	Helicase/polymerase/peptidase polyprotein, Calicivirus-type	Family
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR044067	Picornavirales 3C/3C-like protease domain	Domain
A	IPR033703	Picornavirus/Calicivirus coat protein	Domain
A	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A	IPR000605	Helicase, superfamily 3, single-stranded DNA/RNA virus	Domain
A	IPR037080	Capsid protein VP4 superfamily, Picornavirus	Homologous Superfamily
B	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
B	IPR000199	Peptidase C3A/C3B, picornaviral	Domain
B	IPR001676	Picornavirus capsid	Domain
B	IPR014759	Helicase, superfamily 3, single-stranded RNA virus	Domain
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR029053	Viral coat protein subunit	Homologous Superfamily
B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B	IPR004004	Helicase/polymerase/peptidase polyprotein, Calicivirus-type	Family
B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B	IPR044067	Picornavirales 3C/3C-like protease domain	Domain
B	IPR033703	Picornavirus/Calicivirus coat protein	Domain
B	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
B	IPR000605	Helicase, superfamily 3, single-stranded DNA/RNA virus	Domain
B	IPR037080	Capsid protein VP4 superfamily, Picornavirus	Homologous Superfamily
C	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
C	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
C	IPR000199	Peptidase C3A/C3B, picornaviral	Domain
C	IPR001676	Picornavirus capsid	Domain
C	IPR014759	Helicase, superfamily 3, single-stranded RNA virus	Domain
C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C	IPR029053	Viral coat protein subunit	Homologous Superfamily
C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C	IPR004004	Helicase/polymerase/peptidase polyprotein, Calicivirus-type	Family
C	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C	IPR044067	Picornavirales 3C/3C-like protease domain	Domain
C	IPR033703	Picornavirus/Calicivirus coat protein	Domain
C	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
C	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
C	IPR000605	Helicase, superfamily 3, single-stranded DNA/RNA virus	Domain
C	IPR037080	Capsid protein VP4 superfamily, Picornavirus	Homologous Superfamily