4WSB | pdb_00004wsb

Bat Influenza A polymerase with bound vRNA promoter

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
A	d4wsba1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	PA N-terminal domain	PA N-terminal domain	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
A	d4wsba3	Multi-domain proteins (alpha and beta)	PA C-terminal domain-like	PA C-terminal domain-like	PA C-terminal domain-like	PA C-terminal domain	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
A	d4wsba2	Peptides	Influenza virus PA linker region-like	Influenza virus PA/P3 linker region-like	Influenza virus PA/P3 linker region	PA linker region	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
A	d4wsba4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
B	d4wsbb_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Influenza virus PB1	Polymerase basic protein 1, PB1	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
C	d4wsbc1	Alpha and beta proteins (a+b)	PB2 C-terminal domain-like	PB2 C-terminal domain-like	PB2 C-terminal domain-like	Polymerase basic protein 2, PB2	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
C	d4wsbc2	Alpha and beta proteins (a+b)	Influenza virus PB2 '627' domain-like	Influenza virus PB2 '627' domain-like	Influenza virus PB2 '627' domain	Polymerase basic protein 2, PB2	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
C	d4wsbc3	Alpha and beta proteins (a+b)	Influenza virus PB2 cap binding domain-like	Influenza virus PB2 cap binding domain-like	Influenza virus PB2 cap binding domain	Polymerase basic protein 2, PB2	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
C	d4wsbc6	Multi-domain proteins (alpha and beta)	Influenza virus PB2 N-terminal region	Influenza virus PB2 N-terminal region	Influenza virus PB2 N-terminal region	Polymerase basic protein 2, PB2	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
C	d4wsbc4	Peptides	Influenza virus PB2 linker region-like	Influenza virus PB2 linker region-like	Influenza virus PB2 linker region	Polymerase basic protein 2, PB2	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
C	d4wsbc5	Peptides	Influenza virus PB2 linker region-like	Influenza virus PB2 mid domain-like	Influenza virus PB2 mid domain	Polymerase basic protein 2, PB2	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)
C	d4wsbc7	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) ) [TaxId: 1129347 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Myosin_head	e4wsbA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: Myosin_head	ECOD (develop294)
B	Flu_PB1	e4wsbB1	A: alpha bundles	X: PDEase-like	H: HD-domain/PDEase-like	T: HD-domain/PDEase-like	F: Flu_PB1	ECOD (develop294)
B	Cas3_HD	e4wsbB2	A: alpha bundles	X: PDEase-like	H: HD-domain/PDEase-like	T: HD-domain/PDEase-like	F: Cas3_HD	ECOD (develop294)
C	Flu_PB2_1st	e4wsbC1	A: alpha bundles	X: RNA polymerase PB2 N-terminal fragment	H: RNA polymerase PB2 N-terminal fragment	T: RNA polymerase PB2 N-terminal fragment	F: Flu_PB2_1st	ECOD (develop294)
C	Flu_PB2_2nd	e4wsbC2	A: alpha bundles	X: a+b domain in PB2	H: a+b domain in PB2	T: a+b domain in PB2	F: Flu_PB2_2nd	ECOD (develop294)
C	Flu_PB2_3rd	e4wsbC3	A: alpha bundles	X: Middle domain in PB2	H: Middle domain in PB2	T: Middle domain in PB2	F: Flu_PB2_3rd	ECOD (develop294)
C	Flu_PB2_5th	e4wsbC4	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Flu_PB2_5th	ECOD (develop294)
C	C2	e4wsbC6	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: C2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.91.90	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease	Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00603	Influenza RNA-dependent RNA polymerase subunit PA (Flu_PA)	Influenza RNA-dependent RNA polymerase subunit PA	-	Family
B	PF00602	Influenza RNA-dependent RNA polymerase subunit PB1 (Flu_PB1)	Influenza RNA-dependent RNA polymerase subunit PB1	-	Family
C	PF20948	Influenza RNA polymerase PB2 second domain (Flu_PB2_2nd)	Influenza RNA polymerase PB2 second domain	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase ...	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the domain of the Flu PB protein that follows the N-terminal extended region.	Domain
C	PF00604	Influenza RNA polymerase PB2 CAP binding domain (Flu_PB2_5th)	Influenza RNA polymerase PB2 CAP binding domain	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase ...	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the CAP binding domain [2].	Domain
C	PF20947	Influenza RNA polymerase PB2 N-terminal region (Flu_PB2_1st)	Influenza RNA polymerase PB2 N-terminal region	-	Family
C	PF20949	Influenza RNA polymerase PB2 middle domain (Flu_PB2_3rd)	Influenza RNA polymerase PB2 middle domain	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase ...	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the middle domain in Flu PB2 protein.	Domain
C	PF20951	Influenza RNA polymerase PB2 6th domain (Flu_PB2_6th)	Influenza RNA polymerase PB2 6th domain	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase ...	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the 6th domain of PB2.	Domain
C	PF20950	Influenza RNA polymerase PB2 helical domain (Flu_PB2_4th)	Influenza RNA polymerase PB2 helical domain	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase ...	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the helical domain of Flu PB2 protein.	Domain
C	PF20952	Influenza RNA polymerase PB2 C-terminal domain (Flu_PB2_7th)	Influenza RNA polymerase PB2 C-terminal domain	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase ...	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the C-terminal domain of Flu PB2 protein.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Polymerase PA	RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	viral gene expression viral process viral translational frameshifting viral translation 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 viral gene expression viral process viral translational frameshifting viral translation 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 metabolic process cellular process macromolecule metabolic process symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms 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	-
B	RNA-directed RNA polymerase catalytic subunit	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 binding binding nucleic acid binding guanyl nucleotide binding GTP 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 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 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 viral gene expression viral transcription symbiont-mediated suppression of host gene expression	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle host cell cytoplasm
C	Polymerase PB2	RNA binding binding nucleic acid 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 viral gene expression cap snatching negative stranded viral RNA transcription viral 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 viral gene expression cap snatching negative stranded viral RNA transcription viral process viral transcription RNA-templated viral transcription symbiont-mediated suppression of host gene expression 7-methylguanosine mRNA capping RNA metabolic process primary metabolic process 7-methylguanosine RNA capping RNA capping gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 5'-end processing metabolic process cellular process RNA processing macromolecule metabolic process DNA-templated transcription	host intracellular membrane-bounded organelle host cellular component host intracellular part other organism part host cell mitochondrion host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell nucleus virion component
D [auth R]	Influenza A polymerase vRNA promoter 3' end	-	-	-
E [auth V]	Influenza A polymerase vRNA promoter 5' end	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001009	Influenza RNA-dependent RNA polymerase subunit PA	Family
A	IPR038372	Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain	Homologous Superfamily
B	IPR007099	RNA-directed RNA polymerase, negative-strand RNA virus	Domain
B	IPR001407	Influenza RNA-dependent RNA polymerase subunit PB1	Family
C	IPR049106	Influenza RNA polymerase PB2, N-terminal region	Domain
C	IPR049115	Influenza RNA polymerase PB2, C-terminal domain	Domain
C	IPR049110	Influenza RNA polymerase PB2, second domain	Domain
C	IPR049114	Influenza RNA polymerase PB2, sixth domain	Domain
C	IPR049113	Polymerase basic protein 2, helical domain	Domain
C	IPR049111	Influenza RNA polymerase PB2, middle domain	Domain
C	IPR048298	Influenza RNA polymerase PB2, CAP binding domain	Domain
C	IPR037258	PB2, C-terminal	Homologous Superfamily

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.