2IJD | pdb_00002ijd

Crystal Structure of the Poliovirus Precursor Protein 3CD

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth 2]	d2ijd21	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Viral cysteine protease of trypsin fold	3C cysteine protease (picornain 3C)	(Human poliovirus 1 Mahoney ) [TaxId: 12081 ],	SCOPe (2.08)
B [auth 2]	d2ijd22	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	Viral RNA polymerase	(Human poliovirus 1 Mahoney ) [TaxId: 12081 ],	SCOPe (2.08)
A [auth 1]	d2ijd11	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Viral cysteine protease of trypsin fold	3C cysteine protease (picornain 3C)	(Human poliovirus 1 Mahoney ) [TaxId: 12081 ],	SCOPe (2.08)
A [auth 1]	d2ijd12	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	Viral RNA polymerase	(Human poliovirus 1 Mahoney ) [TaxId: 12081 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth 2]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8038818	3001272	SCOP2B (2022-06-29)
B [auth 2]	SCOP2B Superfamily	Trypsin-like serine proteases	8040974	3000114	SCOP2B (2022-06-29)
B [auth 2]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8038818	3001272	SCOP2B (2022-06-29)
A [auth 1]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8038818	3001272	SCOP2B (2022-06-29)
A [auth 1]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8038818	3001272	SCOP2B (2022-06-29)
A [auth 1]	SCOP2B Superfamily	Trypsin-like serine proteases	8040974	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)
B [auth 2]	tRNA-synt_1_2	e2ijd21	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: tRNA-synt_1_2	ECOD (v294.1)
B [auth 2]	TFR_dimer	e2ijd22	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: TFR_dimer	ECOD (v294.1)
B [auth 2]	RNase_P_Rpp14	e2ijd23	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
A [auth 1]	tRNA-synt_1_2	e2ijd11	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: tRNA-synt_1_2	ECOD (v294.1)
A [auth 1]	TFR_dimer	e2ijd12	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: TFR_dimer	ECOD (v294.1)
A [auth 1]	RNase_P_Rpp14	e2ijd13	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth 2]	2.40.10.120	Mainly Beta	Beta Barrel	Thrombin, subunit H		CATH (4.3.0)
A [auth 1]	2.40.10.120	Mainly Beta	Beta Barrel	Thrombin, subunit H		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth 1], B [auth 2]	PF00548	3C cysteine protease (picornain 3C) (Peptidase_C3)	3C cysteine protease (picornain 3C)	-	Family
A [auth 1], B [auth 2]	PF00680	Viral RNA-dependent RNA polymerase (RdRP_1)	Viral RNA-dependent RNA polymerase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 1], B [auth 2]	Picornain 3C, RNA-directed RNA polymerase	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase 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 cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase 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 transferase activity, transferring phosphorus-containing groups RNA binding binding nucleic acid 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 pyrophosphatase 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 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 structural molecule activity cation binding transition metal ion binding zinc ion binding metal ion binding	symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host translation initiation 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 RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host translation initiation 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 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 transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization gene expression DNA-templated transcription 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 signal transduction pathway 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 perturbation of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane symbiont genome entry into host cell via pore formation in plasma membrane symbiont entry into host cell symbiont entry into host disruption of anatomical structure in another organism virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host endocytosis involved in viral entry into host cell symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity proteolysis protein metabolic process symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity symbiont-mediated perturbation of host intracellular transport symbiont-mediated suppression of host mRNA export from nucleus symbiont-mediated suppression of host gene expression	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component T=pseudo3 icosahedral viral capsid host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 1], B [auth 2]	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A [auth 1], B [auth 2]	IPR002527	Picornavirus 2B protein	Domain
A [auth 1], B [auth 2]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A [auth 1], B [auth 2]	IPR003138	Picornavirus coat protein VP4	Family
A [auth 1], B [auth 2]	IPR000199	Peptidase C3A/C3B, picornaviral	Domain
A [auth 1], B [auth 2]	IPR001676	Picornavirus capsid	Domain
A [auth 1], B [auth 2]	IPR014759	Helicase, superfamily 3, single-stranded RNA virus	Domain
A [auth 1], B [auth 2]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth 1], B [auth 2]	IPR000081	Peptidase C3, picornavirus core protein 2A	Domain
A [auth 1], B [auth 2]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A [auth 1], B [auth 2]	IPR029053	Viral coat protein subunit	Homologous Superfamily
A [auth 1], B [auth 2]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth 1], B [auth 2]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A [auth 1], B [auth 2]	IPR044067	Picornavirales 3C/3C-like protease domain	Domain
A [auth 1], B [auth 2]	IPR033703	Picornavirus/Calicivirus coat protein	Domain
A [auth 1], B [auth 2]	IPR014838	Poliovirus 3A protein-like	Domain
A [auth 1], B [auth 2]	IPR036203	Poliovirus core protein 3a, soluble domain	Homologous Superfamily
A [auth 1], B [auth 2]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A [auth 1], B [auth 2]	IPR000605	Helicase, superfamily 3, single-stranded DNA/RNA virus	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.