7N1H

CryoEM structure of Venezuelan equine encephalitis virus VLP in complex with the LDLRAD3 receptor

External Resource: Annotation

Domain Annotation: ECOD Classification
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 O]	Ldl_recept_a	e7n1hO1	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 M]	Ldl_recept_a	e7n1hM1	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)
C [auth N]	Ldl_recept_a	e7n1hN1	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)
D [auth P]	Ldl_recept_a	e7n1hP1	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)
E [auth D]	Alpha_E1_glycop_2nd	e7n1hD2	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 D]	Alpha_E1_glycop_1st	e7n1hD1	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 D]	Alpha_E1_glycop_like	e7n1hD3	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)
H [auth C]	Alpha_E1_glycop_2nd	e7n1hC2	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)
H [auth C]	Alpha_E1_glycop_1st	e7n1hC1	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)
H [auth C]	Alpha_E1_glycop_like	e7n1hC3	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)
K [auth B]	Alpha_E1_glycop_2nd	e7n1hB2	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)
K [auth B]	Alpha_E1_glycop_1st	e7n1hB1	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)
K [auth B]	Alpha_E1_glycop_like	e7n1hB3	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)
N [auth A]	Alpha_E1_glycop_2nd	e7n1hA2	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)
N [auth A]	Alpha_E1_glycop_1st	e7n1hA1	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)
N [auth A]	Alpha_E1_glycop_like	e7n1hA3	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)
G [auth L]	Peptidase_S3	e7n1hL1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
J [auth K]	Peptidase_S3	e7n1hK1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
M [auth J]	Peptidase_S3	e7n1hJ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
P [auth I]	Peptidase_S3	e7n1hI1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth O], B [auth M], C [auth N], D [auth P]	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat
E [auth D], H [auth C], K [auth B], N [auth A]	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family
F [auth H], I [auth G], L [auth F], O [auth E]	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
G [auth L], J [auth K], M [auth J], P [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
A [auth O], B [auth M], C [auth N], D [auth P]	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
E [auth D], H [auth C], K [auth B], N [auth A]	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 structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane host cell plasma membrane host cellular component host cell part host cell membrane intracellular anatomical structure cytoplasm host intracellular part host cell cytoplasm host intracellular region virion component cell periphery cellular anatomical structure plasma membrane membrane host cell plasma membrane host cellular component host cell part host cell membrane intracellular anatomical structure cytoplasm host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid
F [auth H], I [auth G], L [auth F], O [auth E]	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 structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane host cell plasma membrane host cellular component host cell part host cell membrane intracellular anatomical structure cytoplasm host intracellular part host cell cytoplasm host intracellular region virion component cell periphery cellular anatomical structure plasma membrane membrane host cell plasma membrane host cellular component host cell part host cell membrane intracellular anatomical structure cytoplasm host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid
G [auth L], J [auth K], M [auth J], P [auth I]	Capsid	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 structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane host cell plasma membrane host cellular component host cell part host cell membrane intracellular anatomical structure cytoplasm host intracellular part host cell cytoplasm host intracellular region virion component cell periphery cellular anatomical structure plasma membrane membrane host cell plasma membrane host cellular component host cell part host cell membrane intracellular anatomical structure cytoplasm host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid

InterPro: Protein Family Classification InterPro Database Homepage

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