7X4K | pdb_00007x4k

Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (classified from CVB1 mature virion in complex with 8A10 and 9A3)

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody 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)
E [auth C]	Rhv_3	e7x4kC1	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)
D [auth B]	Rhv_1	e7x4kB1	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 [auth A]	Rhv_5	e7x4kA1	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 [auth L]	V-set	e7x4kL1	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)
A [auth H]	V-set_12	e7x4kH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L]	Light Chain	IGKV4	Kappa	genome polyprotein \| vp3	SAbDab (2026-01-23)
A [auth H]	Heavy Chain	IGHV7	-	genome polyprotein \| vp3	SAbDab (2026-01-23)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth C]	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 pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides 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 ATP-dependent activity structural molecule activity cation binding transition metal ion binding zinc ion 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 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 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 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 cellular process symbiont-mediated perturbation of host process symbiont-mediated perturbation of host autophagy modulation of process of another organism symbiont-mediated activation of host autophagy symbiont-mediated perturbation of host defense response 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 perturbation of host immune response 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 proteolysis protein metabolic process symbiont-mediated perturbation of host intracellular transport symbiont-mediated suppression of host mRNA export from nucleus symbiont-mediated suppression of host gene expression symbiont-mediated perturbation of host gene expression	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle 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 host cell cytoplasmic vesicle membrane other organism part 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
D [auth B]	Genome polyprotein	structural molecule activity	symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms 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 genome entry into host cell via pore formation in plasma membrane symbiont entry into host cell viral process symbiont entry into host disruption of anatomical structure in another organism virion attachment to host cell adhesion of symbiont to host cell symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms 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 genome entry into host cell via pore formation in plasma membrane symbiont entry into host cell viral process 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 cellular process symbiont-mediated suppression of host gene expression symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism	viral capsid virion component host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part
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	host cellular component cellular anatomical structure host cell other organism part viral capsid virion component
B [auth L]	9A3 light chain	-	-	-
A [auth H]	9A3 heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
D [auth B]	IPR029053	Viral coat protein subunit	Homologous Superfamily
D [auth B]	IPR003138	Picornavirus coat protein VP4	Family
D [auth B]	IPR001676	Picornavirus capsid	Domain
D [auth B]	IPR033703	Picornavirus/Calicivirus coat protein	Domain
D [auth B]	IPR036988	Picornavirus coat protein VP4 superfamily	Homologous Superfamily
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