7X2G

Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb nAb 2E6 (CVB1-E:2E6)

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth L]	V-set	e7x2gL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B [auth H]	V-set_8	e7x2gH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth A]	Rhv_5	e7x2gA1	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)
D [auth B]	Rhv_1	e7x2gB1	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)
E [auth C]	Rhv_3	e7x2gC1	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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGKV12	Kappa	vp2	SAbDab (2024-11-08)
B [auth H]	Heavy Chain	IGHV2	-	vp2	SAbDab (2024-11-08)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth 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
E [auth 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 [auth L]	2E6 light chain	-	-	-
B [auth H]	2E6 heavy chain	-	-	-
C [auth A]	Virion protein 1	structural molecule activity	virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	-
D [auth B]	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 organic cyclic compound 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 primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process cellular 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 cellular process 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 biological process involved in interspecies interaction between organisms biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host membrane symbiont genome entry into host cell via pore formation in plasma membrane symbiont-mediated disruption of host cellular anatomical entity 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 symbiont-mediated perturbation of host defense response response to host defenses response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response response to biotic stimulus symbiont-mediated perturbation of host process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process import into cell vesicle-mediated transport endocytosis involved in viral entry into host cell endocytosis transport of virus symbiont-mediated perturbation of host cellular process catabolic process regulation of cellular process autophagy positive regulation of biological process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy regulation of biological process modulation by virus of host autophagy biological regulation regulation of cellular metabolic process regulation of catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process regulation of metabolic process symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway proteolysis protein metabolic process symbiont-mediated suppression of host mRNA export from nucleus symbiont-mediated suppression of host gene expression symbiont-mediated perturbation of host gene expression	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region membrane-bounded organelle intracellular anatomical structure host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane viral capsid icosahedral viral capsid virion component T=pseudo3 icosahedral viral capsid host cell nucleus
E [auth C]	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 organic cyclic compound 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 primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process cellular 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 cellular process 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 biological process involved in interspecies interaction between organisms biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host membrane symbiont genome entry into host cell via pore formation in plasma membrane symbiont-mediated disruption of host cellular anatomical entity 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 symbiont-mediated perturbation of host defense response response to host defenses response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response response to biotic stimulus symbiont-mediated perturbation of host process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process import into cell vesicle-mediated transport endocytosis involved in viral entry into host cell endocytosis transport of virus symbiont-mediated perturbation of host cellular process catabolic process regulation of cellular process autophagy positive regulation of biological process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy regulation of biological process modulation by virus of host autophagy biological regulation regulation of cellular metabolic process regulation of catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process regulation of metabolic process symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway proteolysis protein metabolic process symbiont-mediated suppression of host mRNA export from nucleus symbiont-mediated suppression of host gene expression symbiont-mediated perturbation of host gene expression	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region membrane-bounded organelle intracellular anatomical structure host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane 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
C [auth A]	IPR029053	Viral coat protein subunit	Homologous Superfamily
C [auth A]	IPR001676	Picornavirus capsid	Domain
C [auth A]	IPR033703	Picornavirus/Calicivirus coat protein	Domain
D [auth B]	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
D [auth B]	IPR002527	Picornavirus 2B protein	Domain
D [auth B]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
D [auth B]	IPR036988	Picornavirus coat protein VP4 superfamily	Homologous Superfamily
D [auth B]	IPR003593	AAA+ ATPase domain	Domain
D [auth B]	IPR003138	Picornavirus coat protein VP4	Family
D [auth B]	IPR000199	Peptidase C3A/C3B, picornaviral	Domain
D [auth B]	IPR001676	Picornavirus capsid	Domain
D [auth B]	IPR014759	Helicase, superfamily 3, single-stranded RNA virus	Domain
D [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D [auth B]	IPR000081	Peptidase C3, picornavirus core protein 2A	Domain
D [auth B]	IPR029053	Viral coat protein subunit	Homologous Superfamily
D [auth B]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
D [auth B]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
D [auth B]	IPR044067	Picornavirales 3C/3C-like protease domain	Domain
D [auth B]	IPR033703	Picornavirus/Calicivirus coat protein	Domain
D [auth B]	IPR014838	Poliovirus 3A protein-like	Domain
D [auth B]	IPR036203	Poliovirus core protein 3a, soluble domain	Homologous Superfamily
D [auth B]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
D [auth B]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
D [auth B]	IPR000605	Helicase, superfamily 3, single-stranded DNA/RNA virus	Domain
E [auth C]	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
E [auth C]	IPR002527	Picornavirus 2B protein	Domain
E [auth C]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
E [auth C]	IPR036988	Picornavirus coat protein VP4 superfamily	Homologous Superfamily
E [auth C]	IPR003593	AAA+ ATPase domain	Domain
E [auth C]	IPR003138	Picornavirus coat protein VP4	Family
E [auth C]	IPR000199	Peptidase C3A/C3B, picornaviral	Domain
E [auth C]	IPR001676	Picornavirus capsid	Domain
E [auth C]	IPR014759	Helicase, superfamily 3, single-stranded RNA virus	Domain
E [auth C]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
E [auth C]	IPR000081	Peptidase C3, picornavirus core protein 2A	Domain
E [auth C]	IPR029053	Viral coat protein subunit	Homologous Superfamily
E [auth C]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
E [auth C]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
E [auth C]	IPR044067	Picornavirales 3C/3C-like protease domain	Domain
E [auth C]	IPR033703	Picornavirus/Calicivirus coat protein	Domain
E [auth C]	IPR014838	Poliovirus 3A protein-like	Domain
E [auth C]	IPR036203	Poliovirus core protein 3a, soluble domain	Homologous Superfamily
E [auth C]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
E [auth C]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
E [auth C]	IPR000605	Helicase, superfamily 3, single-stranded DNA/RNA virus	Domain