7FFN | pdb_00007ffn

Cryo-EM structure of VEEV VLP-LDLRAD3-D1 complex at the 5-fold axes

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth K]	SCOP2B Superfamily	Trypsin-like serine proteases	8044424	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)
E [auth O]	Alpha_E1_glycop_2nd	e7ffnO2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E1_glycop_2nd	ECOD (1.6)
E [auth O]	Alpha_E1_glycop_1st	e7ffnO1	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: Alpha_E1_glycop_1st	ECOD (1.6)
E [auth O]	Alpha_E1_glycop_like	e7ffnO3	A: extended segments	X: Transmembrane helix of E1 envelope glycoprotein (From Topology)	H: Transmembrane helix of E1 envelope glycoprotein (From Topology)	T: Transmembrane helix of E1 envelope glycoprotein	F: Alpha_E1_glycop_like	ECOD (1.6)
C [auth M]	Ldl_recept_a	e7ffnM1	A: few secondary structure elements	X: EGF-like	H: LDL receptor-like module (From Topology)	T: LDL receptor-like module	F: Ldl_recept_a	ECOD (1.6)
B [auth L]	Alpha_E3_glycop	e7ffnL1	A: a+b two layers	X: Glycoprotein E3 (From Topology)	H: Glycoprotein E3 (From Topology)	T: Glycoprotein E3	F: Alpha_E3_glycop	ECOD (1.6)
A [auth K]	Peptidase_S3	e7ffnK1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth O]	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (utative)
D [auth N]	2.60.40.3200	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, A domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth O]	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family
D [auth N]	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
C [auth M]	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat
B [auth L]	PF01563	Alphavirus E3 glycoprotein (Alpha_E3_glycop)	Alphavirus E3 glycoprotein	-	Family
A [auth K]	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
E [auth O]	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 structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 symbiont-mediated suppression of host signal transduction pathway 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 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway 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 cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell 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 host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle viral membrane viral envelope
D [auth N]	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 structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 symbiont-mediated suppression of host signal transduction pathway 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 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway 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 cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell 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 host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle viral membrane viral envelope
C [auth M]	Low-density lipoprotein receptor class A domain-containing protein 3	amide binding amyloid-beta binding binding peptide binding	regulation of protein maturation regulation of cellular process regulation of primary metabolic process protein maturation regulation of proteolysis proteolysis protein metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression regulation of protein maturation regulation of cellular process regulation of primary metabolic process protein maturation regulation of proteolysis proteolysis protein metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of protein processing protein processing metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process localization import into cell transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport	cell periphery cellular anatomical structure plasma membrane membrane
B [auth L]	assembly protein E3	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 structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 symbiont-mediated suppression of host signal transduction pathway 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 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway 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 cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell 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 host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle viral membrane viral envelope
A [auth K]	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 structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 symbiont-mediated suppression of host signal transduction pathway 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 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 symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway 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 cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell 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 host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle viral membrane viral envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth O]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
E [auth O]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
E [auth O]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
E [auth O]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
E [auth O]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
E [auth O]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
E [auth O]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
E [auth O]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
E [auth O]	IPR000936	Alphavirus E2 glycoprotein	Family
E [auth O]	IPR000930	Peptidase S3, togavirin	Domain
E [auth O]	IPR002548	Alphavirus E1 glycoprotein	Domain
E [auth O]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth O]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
D [auth N]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
D [auth N]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
D [auth N]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
D [auth N]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
D [auth N]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
D [auth N]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
D [auth N]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
D [auth N]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
D [auth N]	IPR000936	Alphavirus E2 glycoprotein	Family
D [auth N]	IPR000930	Peptidase S3, togavirin	Domain
D [auth N]	IPR002548	Alphavirus E1 glycoprotein	Domain
D [auth N]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth N]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
C [auth M]	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
C [auth M]	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
C [auth M]	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
C [auth M]	IPR050685	Low-density lipoprotein receptor	Family
B [auth L]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
B [auth L]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
B [auth L]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B [auth L]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
B [auth L]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
B [auth L]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B [auth L]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
B [auth L]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
B [auth L]	IPR000936	Alphavirus E2 glycoprotein	Family
B [auth L]	IPR000930	Peptidase S3, togavirin	Domain
B [auth L]	IPR002548	Alphavirus E1 glycoprotein	Domain
B [auth L]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth L]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A [auth K]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
A [auth K]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A [auth K]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A [auth K]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
A [auth K]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A [auth K]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth K]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
A [auth K]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
A [auth K]	IPR000936	Alphavirus E2 glycoprotein	Family
A [auth K]	IPR000930	Peptidase S3, togavirin	Domain
A [auth K]	IPR002548	Alphavirus E1 glycoprotein	Domain
A [auth K]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth K]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth M]	Pharos: Q86YD5	pituitary cancer substance abuse Substance Use Disorders tuberculosis astrocytic tumor drug dependence glioblastoma large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia substance-related disorder ulcerative colitis atypical teratoid rhabdoid tumor interstitial cystitis malignant ependymoma pituitary cancer substance abuse Substance Use Disorders tuberculosis astrocytic tumor drug dependence glioblastoma large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia substance-related disorder ulcerative colitis atypical teratoid rhabdoid tumor interstitial cystitis malignant ependymoma myopathy ovarian cancer pilocytic astrocytoma primitive neuroectodermal tumor substance dependence juvenile idiopathic arthritis malignant glioma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth K], B [auth L], C [auth M], D [auth N], E [auth O]	OPM	Transmembrane	Bitopic proteins	Viral membrane fusion glycoprotein	Alphavirus E1 glycoprotein