4JGZ

Crystal structure of human coxsackievirus A16 uncoating intermediate (space group I222)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
A	d4jgza_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Coxsackievirus A16 ) [TaxId: 31704 ],	SCOPe (2.08)
B	d4jgzb_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Coxsackievirus A16 ) [TaxId: 31704 ],	SCOPe (2.08)
C	d4jgzc_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Coxsackievirus A16 ) [TaxId: 31704 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8068036	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)
A	Rhv_5	e4jgzA1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Rhv_5	ECOD (1.6)
B	Rhv_1	e4jgzB2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Rhv_1	ECOD (1.6)
C	Rhv_3	e4jgzC2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Rhv_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Provenance Source (Version)
A	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls	CATH (4.3.0)
B	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls	CATH (4.3.0)
C	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	Polyprotein, capsid protein VP1	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity endopeptidase activity 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 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 helicase activity RNA helicase activity ATP-dependent activity, acting on RNA structural molecule activity cation binding metal ion binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process RNA metabolic process viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process RNA metabolic process viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization gene expression DNA-templated transcription symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane symbiont genome entry into host cell via pore formation in plasma membrane symbiont entry into host cell symbiont entry into host disruption of anatomical structure in another organism virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host endocytosis involved in viral entry into host cell symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy proteolysis protein metabolic process symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity 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 innate immune response symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated perturbation of host intracellular transport symbiont-mediated suppression of host mRNA export from nucleus	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region viral capsid cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component T=pseudo3 icosahedral viral capsid host cell nucleus
B	Polyprotein, capsid protein VP2	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity endopeptidase activity 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 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 helicase activity RNA helicase activity ATP-dependent activity, acting on RNA structural molecule activity cation binding metal ion binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process RNA metabolic process viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process RNA metabolic process viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization gene expression DNA-templated transcription symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane symbiont genome entry into host cell via pore formation in plasma membrane symbiont entry into host cell symbiont entry into host disruption of anatomical structure in another organism virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host endocytosis involved in viral entry into host cell symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy proteolysis protein metabolic process symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity 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 innate immune response symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated perturbation of host intracellular transport symbiont-mediated suppression of host mRNA export from nucleus	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region viral capsid cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component T=pseudo3 icosahedral viral capsid host cell nucleus
C	Polyprotein, capsid protein VP3	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity endopeptidase activity 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 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 helicase activity RNA helicase activity ATP-dependent activity, acting on RNA structural molecule activity cation binding metal ion binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process RNA metabolic process viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process RNA metabolic process viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization gene expression DNA-templated transcription symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane symbiont genome entry into host cell via pore formation in plasma membrane symbiont entry into host cell symbiont entry into host disruption of anatomical structure in another organism virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host endocytosis involved in viral entry into host cell symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy proteolysis protein metabolic process symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity 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 innate immune response symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated perturbation of host intracellular transport symbiont-mediated suppression of host mRNA export from nucleus	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region viral capsid cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component T=pseudo3 icosahedral viral capsid host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A	IPR002527	Picornavirus 2B protein	Domain
A	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A	IPR003593	AAA+ ATPase domain	Domain
A	IPR003138	Picornavirus coat protein VP4	Family
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	IPR000081	Peptidase C3, picornavirus core protein 2A	Domain
A	IPR029053	Viral coat protein subunit	Homologous Superfamily
A	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
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	IPR014838	Poliovirus 3A protein-like	Domain
A	IPR036203	Poliovirus core protein 3a, soluble domain	Homologous Superfamily
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
B	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
B	IPR002527	Picornavirus 2B protein	Domain
B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
B	IPR003593	AAA+ ATPase domain	Domain
B	IPR003138	Picornavirus coat protein VP4	Family
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	IPR000081	Peptidase C3, picornavirus core protein 2A	Domain
B	IPR029053	Viral coat protein subunit	Homologous Superfamily
B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
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	IPR014838	Poliovirus 3A protein-like	Domain
B	IPR036203	Poliovirus core protein 3a, soluble domain	Homologous Superfamily
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
C	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
C	IPR002527	Picornavirus 2B protein	Domain
C	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
C	IPR003593	AAA+ ATPase domain	Domain
C	IPR003138	Picornavirus coat protein VP4	Family
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	IPR000081	Peptidase C3, picornavirus core protein 2A	Domain
C	IPR029053	Viral coat protein subunit	Homologous Superfamily
C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
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	IPR014838	Poliovirus 3A protein-like	Domain
C	IPR036203	Poliovirus core protein 3a, soluble domain	Homologous Superfamily
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