7Y38 | pdb_00007y38

Molecular architecture of the chikungunya virus replication complex

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)
N [auth Y]	F_UNCLASSIFIED	e7y38Y1	A: a+b complex topology	X: Tomato mosaic virus helicase N-terminal domain (From Topology)	H: Tomato mosaic virus helicase N-terminal domain (From Topology)	T: Tomato mosaic virus helicase N-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
N [auth Y]	F_UNCLASSIFIED	e7y38Y3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
N [auth Y]	Viral_helicase1	e7y38Y2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Viral_helicase1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
N [auth Y]	PF01707	Peptidase family C9 (Peptidase_C9)	Peptidase family C9	-	Family
N [auth Y]	PF20896	Tomato mosaic virus helicase, N-terminal domain (ToMV_Hel_N)	Tomato mosaic virus helicase, N-terminal domain	Tomato mosaic virus (ToMV) generates two large replication proteins in the host cell. The smaller one contains the methyltransferase domain and the helicase domain (Hel). This core helicase domain consists of two RecA domains and an N-terminal access ...	Tomato mosaic virus (ToMV) generates two large replication proteins in the host cell. The smaller one contains the methyltransferase domain and the helicase domain (Hel). This core helicase domain consists of two RecA domains and an N-terminal accessory domain (this entry) containing a flexible loop, a long alpha-helix and an antiparallel, six-stranded beta-sheet. This N-terminal domain plays a role in the binding of the host factors TOM1 and ARL8 required for viral replication [1,2]. It is also found in proteins from related virus.	Domain
N [auth Y]	PF01443	Viral superfamily 1 RNA helicase core domain (Viral_helicase1)	Viral superfamily 1 RNA helicase core domain	This entry represents the (+) RNA virus helicase core domain. The (+) RNA virus helicase core contains two RecA-like alpha/beta domains. The N-terminal ATP-binding domain contains a parallel six-stranded alpha-sheet surrounded by four helices on one ...	This entry represents the (+) RNA virus helicase core domain. The (+) RNA virus helicase core contains two RecA-like alpha/beta domains. The N-terminal ATP-binding domain contains a parallel six-stranded alpha-sheet surrounded by four helices on one side and two helices on the other. The C-terminal domain contains a parallel four-stranded beta-sheet sandwiched between two helices on each of its sides. The (+) RNA virus helicase core is likely to bind NTP in cleft between the N terminus of the ATP-binding domain and the beginning of the C-terminal domain [2,5]. Helicase activity for this domain has been demonstrated [1]. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [3].	Domain
M [auth X]	PF00978	RNA dependent RNA polymerase (RdRP_2)	RNA dependent RNA polymerase	-	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF01660	Viral methyltransferase (Vmethyltransf)	Viral methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
O [auth Z]	RNA (5'-R(PCPCP*A)-3')	-	-	-
N [auth Y]	Protease nsP2	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 RNA methyltransferase activity transferase activity, transferring one-carbon groups methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA methyltransferase activity 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 RNA methyltransferase activity transferase activity, transferring one-carbon groups methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA methyltransferase activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity RNA binding binding nucleic acid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides mRNA 5'-triphosphate monophosphatase activity adenyl ribonucleotide binding adenyl nucleotide binding ATP binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds polynucleotide 5'-phosphatase activity phosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity ATP-dependent activity poly(A) RNA polymerase activity adenylyltransferase activity nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity cation binding metal ion binding	symbiont-mediated suppression of host transcription symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression symbiont-mediated perturbation of host transcription modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process symbiont-mediated suppression of host transcription symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression symbiont-mediated perturbation of host transcription modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction 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 suppression of host gene expression mRNA modification mRNA metabolic process RNA modification macromolecule modification symbiont-mediated suppression of host JAK-STAT cascade symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT activity symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity symbiont-mediated perturbation of host signal transduction pathway methylation regulation of cytoskeleton organization regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation regulation of organelle organization cellular component organization organelle organization cellular component organization or biogenesis cytoskeleton organization gene expression DNA-templated transcription 7-methylguanosine mRNA capping 7-methylguanosine RNA capping RNA capping mRNA processing RNA 5'-end processing RNA processing proteolysis protein metabolic process 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	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular membrane-bounded organelle host intracellular part host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular membrane-bounded organelle host intracellular part host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host intracellular region host cell filopodium host cell projection host cell nucleus
M [auth X]	RNA-directed RNA polymerase nsP4	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 RNA methyltransferase activity transferase activity, transferring one-carbon groups methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA methyltransferase activity 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 RNA methyltransferase activity transferase activity, transferring one-carbon groups methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA methyltransferase activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity RNA binding binding nucleic acid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides mRNA 5'-triphosphate monophosphatase activity adenyl ribonucleotide binding adenyl nucleotide binding ATP binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds polynucleotide 5'-phosphatase activity phosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity ATP-dependent activity poly(A) RNA polymerase activity adenylyltransferase activity nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity cation binding metal ion binding	symbiont-mediated suppression of host transcription symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression symbiont-mediated perturbation of host transcription modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process symbiont-mediated suppression of host transcription symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression symbiont-mediated perturbation of host transcription modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction 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 suppression of host gene expression mRNA modification mRNA metabolic process RNA modification macromolecule modification methylation gene expression DNA-templated transcription 7-methylguanosine mRNA capping 7-methylguanosine RNA capping RNA capping mRNA processing RNA 5'-end processing RNA processing proteolysis protein metabolic process	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular membrane-bounded organelle host intracellular part host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular membrane-bounded organelle host intracellular part host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host intracellular region host cell filopodium host cell projection host cell nucleus
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)	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 RNA methyltransferase activity transferase activity, transferring one-carbon groups methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA methyltransferase activity 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 RNA methyltransferase activity transferase activity, transferring one-carbon groups methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA methyltransferase activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity RNA binding binding nucleic acid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides mRNA 5'-triphosphate monophosphatase activity adenyl ribonucleotide binding adenyl nucleotide binding ATP binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds polynucleotide 5'-phosphatase activity phosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity ATP-dependent activity poly(A) RNA polymerase activity adenylyltransferase activity nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity cation binding metal ion binding	symbiont-mediated suppression of host transcription symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression symbiont-mediated perturbation of host transcription modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process symbiont-mediated suppression of host transcription symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression symbiont-mediated perturbation of host transcription modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction 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 suppression of host gene expression mRNA modification mRNA metabolic process RNA modification macromolecule modification symbiont-mediated suppression of host JAK-STAT cascade symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT activity symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity symbiont-mediated perturbation of host signal transduction pathway methylation regulation of cytoskeleton organization regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation regulation of organelle organization cellular component organization organelle organization cellular component organization or biogenesis cytoskeleton organization gene expression DNA-templated transcription 7-methylguanosine mRNA capping 7-methylguanosine RNA capping RNA capping mRNA processing RNA 5'-end processing RNA processing proteolysis protein metabolic process 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	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular membrane-bounded organelle host intracellular part host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular membrane-bounded organelle host intracellular part host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host intracellular region host cell filopodium host cell projection host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
N [auth Y]	IPR047311	RNA-dependent RNA polymerase, togavirus	Domain
N [auth Y]	IPR048891	Non-structural protein 3, zinc-binding domain	Domain
N [auth Y]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
N [auth Y]	IPR002589	Macro domain	Domain
N [auth Y]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
N [auth Y]	IPR002620	Alphavirus nsp2 protease domain	Domain
N [auth Y]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
N [auth Y]	IPR001788	RNA-dependent RNA polymerase, alsuviricetes	Domain
N [auth Y]	IPR002588	Alphavirus-like methyltransferase domain	Domain
N [auth Y]	IPR043472	Macro domain-like	Homologous Superfamily
N [auth Y]	IPR044936	Alphavirus nsP2 protease domain superfamily	Homologous Superfamily
N [auth Y]	IPR049329	Tomato mosaic virus helicase, N-terminal domain	Domain
N [auth Y]	IPR044371	Non-structural protein 3, X-domain-like	Domain
N [auth Y]	IPR027351	(+) RNA virus helicase core domain	Domain
N [auth Y]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
M [auth X]	IPR047311	RNA-dependent RNA polymerase, togavirus	Domain
M [auth X]	IPR048891	Non-structural protein 3, zinc-binding domain	Domain
M [auth X]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
M [auth X]	IPR002589	Macro domain	Domain
M [auth X]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
M [auth X]	IPR002620	Alphavirus nsp2 protease domain	Domain
M [auth X]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
M [auth X]	IPR001788	RNA-dependent RNA polymerase, alsuviricetes	Domain
M [auth X]	IPR002588	Alphavirus-like methyltransferase domain	Domain
M [auth X]	IPR043472	Macro domain-like	Homologous Superfamily
M [auth X]	IPR044936	Alphavirus nsP2 protease domain superfamily	Homologous Superfamily
M [auth X]	IPR049329	Tomato mosaic virus helicase, N-terminal domain	Domain
M [auth X]	IPR044371	Non-structural protein 3, X-domain-like	Domain
M [auth X]	IPR027351	(+) RNA virus helicase core domain	Domain
M [auth X]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR047311	RNA-dependent RNA polymerase, togavirus	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR048891	Non-structural protein 3, zinc-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR002589	Macro domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR002620	Alphavirus nsp2 protease domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR001788	RNA-dependent RNA polymerase, alsuviricetes	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR002588	Alphavirus-like methyltransferase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR043472	Macro domain-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR044936	Alphavirus nsP2 protease domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR049329	Tomato mosaic virus helicase, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR044371	Non-structural protein 3, X-domain-like	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR027351	(+) RNA virus helicase core domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain