1URZ | pdb_00001urz

Low pH induced, membrane fusion conformation of the envelope protein of tick-borne encephalitis virus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d1urzf1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Class II viral fusion proteins C-terminal domain	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
F	d1urzf2	Membrane and cell surface proteins and peptides	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
E	d1urze1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Class II viral fusion proteins C-terminal domain	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
E	d1urze2	Membrane and cell surface proteins and peptides	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
D	d1urzd1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Class II viral fusion proteins C-terminal domain	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
D	d1urzd2	Membrane and cell surface proteins and peptides	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
C	d1urzc1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Class II viral fusion proteins C-terminal domain	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
C	d1urzc2	Membrane and cell surface proteins and peptides	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
B	d1urzb1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Class II viral fusion proteins C-terminal domain	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
B	d1urzb2	Membrane and cell surface proteins and peptides	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
A	d1urza1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Class II viral fusion proteins C-terminal domain	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)
A	d1urza2	Membrane and cell surface proteins and peptides	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Envelope glycoprotein	(Tick-borne encephalitis virus (WESTERN SUBTYPE) ) [TaxId: 11088 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Viral glycoprotein, central and dimerisation domains	8037957	3000293	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	E set domains	8054967	3000070	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	E set domains	8054967	3000070	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Viral glycoprotein, central and dimerisation domains	8037957	3000293	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Viral glycoprotein, central and dimerisation domains	8037957	3000293	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	E set domains	8054967	3000070	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	E set domains	8054967	3000070	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Viral glycoprotein, central and dimerisation domains	8037957	3000293	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Viral glycoprotein, central and dimerisation domains	8037957	3000293	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	E set domains	8054967	3000070	SCOP2B (2022-06-29)
A	SCOP2 Family	Class II viral fusion proteins C-terminal domain	8054968	4007569	SCOP2 (2022-06-29)
A	SCOP2 Family	Viral glycoprotein, central and dimerisation domains	8055443	4003128	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	E set domains	8054969	3000070	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Viral glycoprotein, central and dimerisation domains	8055444	3000293	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Viral glycoprotein, central and dimerisation domains	8037957	3000293	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	E set domains	8054967	3000070	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)
F	Flavi_glycop_C	e1urzF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
F	Flavi_glycoprot	e1urzF2	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: Flavi_glycoprot	ECOD (1.6)
E	Flavi_glycop_C	e1urzE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
E	Flavi_glycoprot	e1urzE2	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: Flavi_glycoprot	ECOD (1.6)
D	Flavi_glycop_C	e1urzD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
D	Flavi_glycoprot	e1urzD2	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: Flavi_glycoprot	ECOD (1.6)
C	Flavi_glycop_C	e1urzC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
C	Flavi_glycoprot	e1urzC2	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: Flavi_glycoprot	ECOD (1.6)
B	Flavi_glycop_C	e1urzB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
B	Flavi_glycoprot	e1urzB2	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: Flavi_glycoprot	ECOD (1.6)
A	Flavi_glycop_C	e1urzA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
A	Flavi_glycoprot	e1urzA2	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: Flavi_glycoprot	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.60.98.10	Mainly Beta	Sandwich	Tick-borne Encephalitis virus Glycoprotein	domain 1	CATH (4.3.0)
F	3.30.67.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 2	CATH (4.3.0)
F	3.30.387.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 3	CATH (4.3.0)
F	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
E	2.60.98.10	Mainly Beta	Sandwich	Tick-borne Encephalitis virus Glycoprotein	domain 1	CATH (4.3.0)
E	3.30.67.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 2	CATH (4.3.0)
E	3.30.387.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 3	CATH (4.3.0)
E	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
D	2.60.98.10	Mainly Beta	Sandwich	Tick-borne Encephalitis virus Glycoprotein	domain 1	CATH (4.3.0)
D	3.30.67.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 2	CATH (4.3.0)
D	3.30.387.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 3	CATH (4.3.0)
D	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C	2.60.98.10	Mainly Beta	Sandwich	Tick-borne Encephalitis virus Glycoprotein	domain 1	CATH (4.3.0)
C	3.30.67.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 2	CATH (4.3.0)
C	3.30.387.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 3	CATH (4.3.0)
C	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B	2.60.98.10	Mainly Beta	Sandwich	Tick-borne Encephalitis virus Glycoprotein	domain 1	CATH (4.3.0)
B	3.30.67.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 2	CATH (4.3.0)
B	3.30.387.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 3	CATH (4.3.0)
B	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.60.98.10	Mainly Beta	Sandwich	Tick-borne Encephalitis virus Glycoprotein	domain 1	CATH (4.3.0)
A	3.30.67.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 2	CATH (4.3.0)
A	3.30.387.10	Alpha Beta	2-Layer Sandwich	Viral Envelope Glycoprotein	domain 3	CATH (4.3.0)
A	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00869	Flavivirus glycoprotein, central and dimerisation domains (Flavi_glycoprot)	Flavivirus glycoprotein, central and dimerisation domains		Domain
A, B, C, D, E A, B, C, D, E, F	PF02832	Flavivirus glycoprotein, immunoglobulin-like domain (Flavi_glycop_C)	Flavivirus glycoprotein, immunoglobulin-like domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	ENVELOPE PROTEIN	RNA binding double-stranded RNA binding binding nucleic acid binding 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 catalytic activity transferase activity, transferring phosphorus-containing groups peptidase activity RNA binding double-stranded RNA binding binding nucleic acid binding 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 catalytic activity transferase activity, transferring phosphorus-containing groups peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity endopeptidase activity 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 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 protein binding protein dimerization activity cation binding metal ion binding RNA methyltransferase activity O-methyltransferase activity methyltransferase cap1 activity transferase activity, transferring one-carbon groups methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity mRNA methyltransferase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides structural molecule activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host JAK-STAT cascade 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 JAK-STAT cascade via inhibition of STAT activity symbiont-mediated perturbation of host process symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity 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 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 protein metabolic process	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system host intracellular region cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane viral capsid virion component host cell perinuclear region of cytoplasm virion membrane extracellular region host cell nucleus viral membrane viral envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR000208	RNA-directed RNA polymerase, fingers/palm subdomains, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001122	Capsid protein C, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014412	Genome polyprotein, Flavivirus	Family
A, B, C, D, E A, B, C, D, E, F	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR011492	Non-structural protein NS3-like, DEAD-box helicase, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR026490	mRNA cap 0/1 methyltransferase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000752	Flavivirus non-structural protein NS2A	Domain
A, B, C, D, E A, B, C, D, E, F	IPR047530	RNA-dependent RNA polymerase, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR049486	Flavivridae NS3 helicase, C-terminal helical domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR046811	RNA-directed RNA polymerase, thumb subdomain, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR002877	Ribosomal RNA methyltransferase, FtsJ domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR038302	Envelope glycoprotein M superfamily, flavivirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000069	Envelope glycoprotein M, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR038688	Flavivirus polyprotein propeptide superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR026470	Flavivirus envelope glycoprotein E, Stem/Anchor domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000404	Flavivirus non-structural protein NS4A	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000487	Non-structural protein NS2B, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001528	Flavivirus non-structural protein NS4B	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001157	Non-structural protein NS1, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001850	Non-structural protein NS3, peptidase S7, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR002535	Flavivirus polyprotein propeptide	Domain
A, B, C, D, E A, B, C, D, E, F	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain