8X0M | pdb_00008x0m

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(5-fold)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J [auth D]	SCOP2B Superfamily	LDL receptor-like module	8035671	3000728	SCOP2B (2022-06-29)
K [auth H]	SCOP2B Superfamily	LDL receptor-like module	8035671	3000728	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Viral glycoprotein, central and dimerisation domains	8037191	3000293	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	E set domains	8054997	3000070	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	E set domains	8054997	3000070	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Viral glycoprotein, central and dimerisation domains	8037191	3000293	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	Viral glycoprotein, central and dimerisation domains	8037191	3000293	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	E set domains	8054997	3000070	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8042286	3000114	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Trypsin-like serine proteases	8042286	3000114	SCOP2B (2022-06-29)
G [auth I]	SCOP2B Superfamily	Trypsin-like serine proteases	8042286	3000114	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
J [auth D], K [auth H]	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat
C, F [auth G], I [auth K]	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family
B, E [auth F], H [auth J]	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
A, D [auth E], G [auth I]	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
J [auth D], K [auth H]	Very low-density lipoprotein receptor	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding reelin receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity apolipoprotein binding protein binding lipoprotein particle receptor activity cargo receptor activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding reelin receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity apolipoprotein binding protein binding lipoprotein particle receptor activity cargo receptor activity very-low-density lipoprotein particle receptor activity low-density lipoprotein particle receptor activity lipoprotein particle binding protein-containing complex binding protein-lipid complex binding very-low-density lipoprotein particle binding calcium-dependent protein binding	multicellular organismal process regulation of biological process very-low-density lipoprotein particle clearance plasma lipoprotein particle clearance biological regulation regulation of plasma lipoprotein particle levels localization transport macromolecule localization lipid localization lipid transport establishment of localization establishment of protein localization nitrogen compound transport multicellular organismal process regulation of biological process very-low-density lipoprotein particle clearance plasma lipoprotein particle clearance biological regulation regulation of plasma lipoprotein particle levels localization transport macromolecule localization lipid localization lipid transport establishment of localization establishment of protein localization nitrogen compound transport protein transport glycoprotein transport intracellular protein localization carbohydrate derivative transport behavior system process learning or memory nervous system process cognition memory cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development cellular process secondary alcohol metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process small molecule metabolic process metabolic process primary metabolic process lipid metabolic process cellular response to stimulus regulation of cellular process response to stimulus signaling signal transduction cell communication spinal cord development central nervous system development ventral spinal cord development cell surface receptor signaling pathway reelin-mediated signaling pathway regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process positive regulation of biological process positive regulation of developmental process positive regulation of neuron projection development positive regulation of cell projection organization positive regulation of cellular process regulation of cell projection organization positive regulation of dendrite development regulation of dendrite development regulation of plasma membrane bounded cell projection organization cellular component biogenesis cellular component assembly cell junction assembly regulation of synapse structure or activity regulation of synapse assembly synapse organization regulation of biological quality regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly import into cell receptor-mediated endocytosis endocytosis vesicle-mediated transport	cellular anatomical structure clathrin-coated pit membrane endomembrane system cell periphery plasma membrane synapse cell junction glutamatergic synapse protein-containing complex receptor complex vacuolar membrane membrane-bounded organelle intracellular anatomical structure cellular anatomical structure clathrin-coated pit membrane endomembrane system cell periphery plasma membrane synapse cell junction glutamatergic synapse protein-containing complex receptor complex vacuolar membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome very-low-density lipoprotein particle extracellular region plasma lipoprotein particle extracellular space triglyceride-rich plasma lipoprotein particle lipoprotein particle protein-lipid complex
C, F [auth G], I [auth K]	Spike glycoprotein E1	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 small molecule binding structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion assembly viral life cycle 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 viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion assembly viral life cycle 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 establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host cellular process 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 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	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host intracellular part cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell endosome host intracellular region host cell nucleus viral membrane viral envelope
B, E [auth F], H [auth J]	Spike glycoprotein E2	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 small molecule binding structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion assembly viral life cycle 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 viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion assembly viral life cycle 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 establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host cellular process 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 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	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host intracellular part cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell endosome host intracellular region host cell nucleus viral membrane viral envelope
A, D [auth E], G [auth I]	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 small molecule binding structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion assembly viral life cycle 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 viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion assembly viral life cycle 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 establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host cellular process 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 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	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host intracellular part cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell endosome host intracellular region host cell nucleus viral membrane viral envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
J [auth D], K [auth H]	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
J [auth D], K [auth H]	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
J [auth D], K [auth H]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
J [auth D], K [auth H]	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
J [auth D], K [auth H]	IPR000742	EGF-like domain	Domain
J [auth D], K [auth H]	IPR049883	NOTCH1 EGF-like calcium-binding domain	Domain
J [auth D], K [auth H]	IPR051221	Low-density lipoprotein receptor-related	Family
J [auth D], K [auth H]	IPR000033	LDLR class B repeat	Repeat
J [auth D], K [auth H]	IPR001881	EGF-like calcium-binding domain	Domain
J [auth D], K [auth H]	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
J [auth D], K [auth H]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
C, F [auth G], I [auth K]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
C, F [auth G], I [auth K]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
C, F [auth G], I [auth K]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
C, F [auth G], I [auth K]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
C, F [auth G], I [auth K]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
C, F [auth G], I [auth K]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C, F [auth G], I [auth K]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
C, F [auth G], I [auth K]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
C, F [auth G], I [auth K]	IPR000936	Alphavirus E2 glycoprotein	Family
C, F [auth G], I [auth K]	IPR000930	Peptidase S3, togavirin	Domain
C, F [auth G], I [auth K]	IPR002548	Alphavirus E1 glycoprotein	Domain
C, F [auth G], I [auth K]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
C, F [auth G], I [auth K]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B, E [auth F], H [auth J]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
B, E [auth F], H [auth J]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
B, E [auth F], H [auth J]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B, E [auth F], H [auth J]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
B, E [auth F], H [auth J]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
B, E [auth F], H [auth J]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B, E [auth F], H [auth J]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
B, E [auth F], H [auth J]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
B, E [auth F], H [auth J]	IPR000936	Alphavirus E2 glycoprotein	Family
B, E [auth F], H [auth J]	IPR000930	Peptidase S3, togavirin	Domain
B, E [auth F], H [auth J]	IPR002548	Alphavirus E1 glycoprotein	Domain
B, E [auth F], H [auth J]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
B, E [auth F], H [auth J]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, D [auth E], G [auth I]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
A, D [auth E], G [auth I]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, D [auth E], G [auth I]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, D [auth E], G [auth I]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
A, D [auth E], G [auth I]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A, D [auth E], G [auth I]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, D [auth E], G [auth I]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
A, D [auth E], G [auth I]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
A, D [auth E], G [auth I]	IPR000936	Alphavirus E2 glycoprotein	Family
A, D [auth E], G [auth I]	IPR000930	Peptidase S3, togavirin	Domain
A, D [auth E], G [auth I]	IPR002548	Alphavirus E1 glycoprotein	Domain
A, D [auth E], G [auth I]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A, D [auth E], G [auth I]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
J [auth D], K [auth H]	Pharos: P98155	obesity disorder cerebellar ataxia, intellectual disability, and dysequilibrium syndrome 1 intellectual disability malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm psoriasis astrocytic tumor ulcerative colitis Autistic Disorder cerebellar ataxia, intellectual disability, and dysequilibrium cerebrovascular disorder invasive ductal breast carcinoma malignant ependymoma medulloblastoma ovarian cancer obesity disorder cerebellar ataxia, intellectual disability, and dysequilibrium syndrome 1 intellectual disability malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm psoriasis astrocytic tumor ulcerative colitis Autistic Disorder cerebellar ataxia, intellectual disability, and dysequilibrium cerebrovascular disorder invasive ductal breast carcinoma malignant ependymoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia breast carcinoma ductal breast carcinoma in situ esophageal adenocarcinoma large cell medulloblastoma malignant mesothelioma myopathy pancreatic intraductal papillary-mucinous carcinoma Pick disease spina bifida autism breast fibroadenoma lung cancer