Annotations: 3J0F

Sindbis virion

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	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)
L	Helicase_C	e3j0fL1	A: alpha arrays	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F: Helicase_C	ECOD (v295.2)
L	Rhodanese	e3j0fL3	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: Alpha helical domain of ribonucleotide reductases	F: Rhodanese	ECOD (v295.2)
K	Helicase_C	e3j0fK1	A: alpha arrays	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F: Helicase_C	ECOD (v295.2)
K	Rhodanese	e3j0fK3	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: Alpha helical domain of ribonucleotide reductases	F: Rhodanese	ECOD (v295.2)
J	Helicase_C	e3j0fJ1	A: alpha arrays	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F: Helicase_C	ECOD (v295.2)
J	Rhodanese	e3j0fJ3	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: Alpha helical domain of ribonucleotide reductases	F: Rhodanese	ECOD (v295.2)
I	Helicase_C	e3j0fI1	A: alpha arrays	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F: Helicase_C	ECOD (v295.2)
I	Rhodanese	e3j0fI3	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: Alpha helical domain of ribonucleotide reductases	F: Rhodanese	ECOD (v295.2)
H	DUF1989	e3j0fH1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DUF1989	ECOD (v295.2)
H	MR_MLE_N	e3j0fH3	A: alpha arrays	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: MR_MLE_N	ECOD (v295.2)
G	DUF1989	e3j0fG1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DUF1989	ECOD (v295.2)
G	MR_MLE_N	e3j0fG3	A: alpha arrays	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: MR_MLE_N	ECOD (v295.2)
F	DUF1989	e3j0fF1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DUF1989	ECOD (v295.2)
F	MR_MLE_N	e3j0fF3	A: alpha arrays	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: MR_MLE_N	ECOD (v295.2)
E	RA	e3j0fE1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RA	ECOD (v295.2)
E	VWA	e3j0fE3	A: alpha arrays	X: DP domain	H: DP domain	T: DP domain	F: VWA	ECOD (v295.2)
D	PNP_UDP_1	e3j0fD1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PNP_UDP_1	ECOD (v295.2)
C	PNP_UDP_1	e3j0fC1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PNP_UDP_1	ECOD (v295.2)
B	PNP_UDP_1	e3j0fB1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PNP_UDP_1	ECOD (v295.2)
A	Sod_Fe_C	e3j0fA1	A: alpha arrays	X: Cytochrome P450	H: Cytochrome P450	T: Cytochrome P450	F: Sod_Fe_C	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I, J, K, L	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
E, F, G, H	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family
A, B, C, D	PF00944	Alphavirus core protein (Peptidase_S3)	Alphavirus core protein	Also known as coat protein C and capsid protein C. This makes the literature very confusing. Alphaviruses consist of a nucleoprotein core, a lipid membrane which envelopes the core, and glycoprotein spikes protruding from the lipid membrane.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, J, K, L	E2 envelope glycoprotein	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral translational frameshifting viral translation transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process receptor-mediated virion attachment to host cell entry receptor-mediated virion attachment to host cell	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component icosahedral viral capsid, spike host cell plasma membrane host cell membrane virion membrane T=4 icosahedral viral capsid host cell Golgi apparatus host cell nucleus viral membrane viral envelope
E, F, G, H	E1 envelope glycoprotein	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral translational frameshifting viral translation transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process receptor-mediated virion attachment to host cell entry receptor-mediated virion attachment to host cell	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component icosahedral viral capsid, spike host cell plasma membrane host cell membrane virion membrane T=4 icosahedral viral capsid host cell Golgi apparatus host cell nucleus viral membrane viral envelope
A, B, C, D	Capsid protein	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral translational frameshifting viral translation transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process receptor-mediated virion attachment to host cell entry receptor-mediated virion attachment to host cell	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component icosahedral viral capsid, spike host cell plasma membrane host cell membrane virion membrane T=4 icosahedral viral capsid host cell Golgi apparatus host cell nucleus viral membrane viral envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I, J, K, L	IPR002533	Alphavirus E3 spike glycoprotein	Domain
I, J, K, L	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
I, J, K, L	IPR014756	Immunoglobulin E-set	Homologous Superfamily
I, J, K, L	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
I, J, K, L	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
I, J, K, L	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
I, J, K, L	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
I, J, K, L	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
I, J, K, L	IPR000936	Alphavirus E2 glycoprotein	Family
I, J, K, L	IPR000930	Peptidase S3, togavirin	Domain
I, J, K, L	IPR002548	Alphavirus E1 glycoprotein	Domain
I, J, K, L	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
E, F, G, H	IPR002533	Alphavirus E3 spike glycoprotein	Domain
E, F, G, H	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
E, F, G, H	IPR014756	Immunoglobulin E-set	Homologous Superfamily
E, F, G, H	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
E, F, G, H	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
E, F, G, H	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
E, F, G, H	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
E, F, G, H	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
E, F, G, H	IPR000936	Alphavirus E2 glycoprotein	Family
E, F, G, H	IPR000930	Peptidase S3, togavirin	Domain
E, F, G, H	IPR002548	Alphavirus E1 glycoprotein	Domain
E, F, G, H	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR002533	Alphavirus E3 spike glycoprotein	Domain
A, B, C, D	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, B, C, D	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B, C, D	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
A, B, C, D	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A, B, C, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
A, B, C, D	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
A, B, C, D	IPR000936	Alphavirus E2 glycoprotein	Family
A, B, C, D	IPR000930	Peptidase S3, togavirin	Domain
A, B, C, D	IPR002548	Alphavirus E1 glycoprotein	Domain
A, B, C, D	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily