4CL1 | pdb_00004cl1

The crystal structure of NS5A domain 1 from genotype 1a reveals new clues to the mechanism of action for dimeric HCV inhibitors

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	PCI	e4cl1A1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F: PCI	ECOD (develop294)
B	PCI	e4cl1B1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F: PCI	ECOD (develop294)
C	PCI	e4cl1C1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F: PCI	ECOD (develop294)
D	PCI	e4cl1D1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F: PCI	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.20.25.210	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	Hepatitis C NS5A, domain 1B	CATH (4.3.0)
A	2.20.25.220	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	Hepatitis C virus NS5A, 1B domain	CATH (4.3.0)
B	2.20.25.210	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	Hepatitis C NS5A, domain 1B	CATH (4.3.0)
B	2.20.25.220	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	Hepatitis C virus NS5A, 1B domain	CATH (4.3.0)
C	2.20.25.210	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	Hepatitis C NS5A, domain 1B	CATH (4.3.0)
C	2.20.25.220	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	Hepatitis C virus NS5A, 1B domain	CATH (4.3.0)
D	2.20.25.210	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	Hepatitis C NS5A, domain 1B	CATH (4.3.0)
D	2.20.25.220	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	Hepatitis C virus NS5A, 1B domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08301	Hepatitis C virus non-structural 5a domain 1b (HCV_NS5a_1b)	Hepatitis C virus non-structural 5a domain 1b	The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR, Swiss:P19525 [1,2]. T ...	The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR, Swiss:P19525 [1,2]. This region corresponds to the 1b domain [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	NON-STRUCTURAL PROTEIN 5A	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 protein binding binding Toll-like receptor 2 binding signaling receptor binding Toll-like receptor 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 protein binding binding Toll-like receptor 2 binding signaling receptor binding Toll-like receptor binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity endopeptidase activity SH3 domain binding protein domain specific binding 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 cysteine-type peptidase activity cysteine-type endopeptidase activity RNA binding nucleic acid binding kinase binding enzyme binding 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 passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity cation binding transition metal ion binding zinc ion binding metal ion binding	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 negative regulation of protein transport regulation of localization establishment of protein localization regulation of cellular process regulation of protein localization transport negative regulation of biological process negative regulation of transport protein localization to extracellular region localization regulation of secretion by cell secretion by cell negative regulation of secretion negative regulation of cellular process negative regulation of secretion by cell intracellular protein localization negative regulation of protein localization regulation of biological process regulation of transport secretion biological regulation regulation of establishment of protein localization establishment of protein localization to extracellular region negative regulation of establishment of protein localization export from cell regulation of protein transport protein secretion establishment of localization regulation of protein secretion regulation of secretion negative regulation of protein secretion protein transport macromolecule localization regulation of cytokinesis positive regulation of cell division regulation of cell cycle process positive regulation of biological process cytokinesis positive regulation of cell cycle regulation of cell division positive regulation of cytokinesis positive regulation of cell cycle process cell division cell cycle regulation of cell cycle positive regulation of cellular process cell cycle 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 suppression of host TRAF-mediated signal transduction symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy regulation of primary metabolic process negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of macromolecule metabolic process gene expression regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated transformation of host cell fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion assembly viral capsid assembly import into cell receptor-mediated endocytosis of virus by host cell vesicle-mediated transport 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 translocation of peptides or proteins into host translocation of molecules into host translocation of peptides or proteins into host cell cytoplasm viral gene expression viral translational frameshifting viral translation transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport positive regulation of phosphorylation regulation of catalytic activity positive regulation of phosphate metabolic process regulation of transferase activity positive regulation of metabolic process positive regulation of molecular function phosphate-containing compound metabolic process phosphorus metabolic process positive regulation of hexokinase activity positive regulation of phosphorus metabolic process phosphorylation positive regulation of catalytic activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of phosphorus metabolic process regulation of phosphorylation virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host innate immune response symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway proteolysis protein metabolic process symbiont-mediated perturbation of host cell cycle progression symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint entry receptor-mediated virion attachment to host cell	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host cell lipid droplet host intracellular region other organism part host cell cytoplasm part host intracellular membrane-bounded organelle host cell membrane host cell mitochondrion host intracellular organelle host cell mitochondrial envelope host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host cell lipid droplet host intracellular region other organism part host cell cytoplasm part host intracellular membrane-bounded organelle host cell membrane host cell mitochondrion host intracellular organelle host cell mitochondrial envelope host cell mitochondrial membrane membrane-bounded organelle intracellular anatomical structure membrane intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment cytoplasm organelle membrane host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane viral nucleocapsid viral capsid virion component host cell plasma membrane host cell perinuclear region of cytoplasm virion membrane host cell nucleus viral membrane viral envelope protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002522	Hepatitis C virus, Core protein, N-terminal	Domain
A, B, C, D	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D	IPR054175	NS3 RNA helicase, C-terminal helical domain	Domain
A, B, C, D	IPR011492	Non-structural protein NS3-like, DEAD-box helicase, flavivirus	Domain
A, B, C, D	IPR038568	Hepatitis C virus NS5A, 1B domain superfamily	Homologous Superfamily
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C, D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C, D	IPR002868	Hepatitis C virus, Non-structural 5a protein	Domain
A, B, C, D	IPR038170	NS5A domain 1a superfamily	Homologous Superfamily
A, B, C, D	IPR002518	Hepatitis C virus, Non-structural protein NS2	Domain
A, B, C, D	IPR013192	Hepatitis C virus, Non-structural 5a protein, domain 1a	Domain
A, B, C, D	IPR002521	Hepatitis C virus, Core protein, C-terminal	Domain
A, B, C, D	IPR042209	Hepatitis C virus non-structural protein NS2, N-terminal domain	Homologous Superfamily
A, B, C, D	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A, B, C, D	IPR000745	Hepatitis C virus, Non-structural protein NS4a	Domain
A, B, C, D	IPR042205	Hepatitis C virus non-structural protein NS2, C-terminal domain	Homologous Superfamily
A, B, C, D	IPR002166	RNA dependent RNA polymerase, hepatitis C virus	Family
A, B, C, D	IPR002519	Hepatitis C virus, Envelope glycoprotein E1	Domain
A, B, C, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D	IPR044896	Hepatitis C virus core protein, chain A superfamily	Homologous Superfamily
A, B, C, D	IPR024350	Hepatitus C virus, Non-structural 5a protein, C-terminal	Domain
A, B, C, D	IPR013193	Hepatitis C virus non-structural 5a, 1B domain	Domain
A, B, C, D	IPR004109	Hepatitis C virus, NS3 protease	Domain
A, B, C, D	IPR049913	Hepatitis C virus, p7 channel	Domain
A, B, C, D	IPR002531	Hepatitis C virus, Non-structural protein E2/NS1	Domain
A, B, C, D	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A, B, C, D	IPR001490	Hepatitis C virus, Non-structural protein NS4b	Domain