6QXE

Influenza A virus (A/NT/60/1968) polymerase dimer of hetermotrimer in complex with 3'5' cRNA promoter and Nb8205

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
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)
D [auth B]	PF00602	e6qxeB2	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: PF00602	ECOD (1.6)
D [auth B]	PF00602	e6qxeB1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: PF00602	ECOD (1.6)
H [auth F]	PF00602	e6qxeF2	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: PF00602	ECOD (1.6)
H [auth F]	PF00602	e6qxeF1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: PF00602	ECOD (1.6)
E [auth C]	PF20948	e6qxeC1	A: a+b two layers	X: a+b domain in PB2 (From Topology)	H: a+b domain in PB2 (From Topology)	T: a+b domain in PB2	F: PF20948	ECOD (1.6)
I [auth G]	PF20948	e6qxeG1	A: a+b two layers	X: a+b domain in PB2 (From Topology)	H: a+b domain in PB2 (From Topology)	T: a+b domain in PB2	F: PF20948	ECOD (1.6)
A [auth M]	PF07686	e6qxeM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth O]	PF07686	e6qxeO1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth M], B [auth O]	Heavy Chain	IGHV3	-	polymerase acidic protein \| rna-directed rna polymerase catalytic subunit	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], G [auth E]	PF00603	Influenza RNA-dependent RNA polymerase subunit PA (Flu_PA)	Influenza RNA-dependent RNA polymerase subunit PA	-	Family
D [auth B], H [auth F]	PF00602	Influenza RNA-dependent RNA polymerase subunit PB1 (Flu_PB1)	Influenza RNA-dependent RNA polymerase subunit PB1	-	Family
E [auth C], I [auth G]	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
E [auth C], I [auth G]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], G [auth E]	Polymerase acidic protein	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	cellular biosynthetic process cellular 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic process cellular biosynthetic process cellular 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic process viral RNA genome replication organic cyclic compound biosynthetic process viral process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process viral gene expression cap snatching negative stranded viral RNA transcription viral transcription RNA-templated viral transcription gene expression DNA-templated transcription symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host transcription symbiont-mediated suppression of host gene expression symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity modulation by symbiont of host process symbiont-mediated perturbation of host gene expression symbiont-mediated perturbation of host transcription modulation of process of another organism	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell part host intracellular region cellular anatomical entity host cell nucleus host intracellular organelle host cell cytoplasm
D [auth B], H [auth F]	RNA-directed RNA polymerase catalytic subunit	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding organic cyclic compound binding nucleic acid binding nucleoside phosphate binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding organic cyclic compound binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	cellular biosynthetic process cellular 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic process cellular biosynthetic process cellular 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic process viral RNA genome replication organic cyclic compound biosynthetic process viral process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process viral gene expression viral transcription gene expression DNA-templated transcription symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host transcription symbiont-mediated suppression of host gene expression symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity modulation by symbiont of host process symbiont-mediated perturbation of host gene expression symbiont-mediated perturbation of host transcription modulation of process of another organism	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell part host intracellular region cellular anatomical entity host cell nucleus host intracellular organelle host cell cytoplasm
E [auth C], I [auth G]	Polymerase basic protein 2	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding organic cyclic compound binding nucleic acid binding	cellular biosynthetic process cellular 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic process cellular biosynthetic process cellular 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic process viral RNA genome replication organic cyclic compound biosynthetic process viral process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process viral gene expression cap snatching negative stranded viral RNA transcription viral transcription RNA-templated viral transcription symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host transcription symbiont-mediated suppression of host gene expression symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity modulation by symbiont of host process symbiont-mediated perturbation of host gene expression symbiont-mediated perturbation of host transcription modulation of process of another organism 7-methylguanosine RNA capping RNA capping mRNA processing RNA processing 7-methylguanosine mRNA capping gene expression mRNA metabolic process RNA 5'-end processing DNA-templated transcription symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated perturbation of host defense response response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell mitochondrion host cell cytoplasm part host intracellular organelle host cell nucleus virion component
F [auth D], J [auth H]	RNA (5'-R(PAPGPCPAPAPAPAPGPCPAPGPG)-3')	-	-	-
A [auth M], B [auth O]	Nb8205	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], G [auth E]	IPR001009	Influenza RNA-dependent RNA polymerase subunit PA	Family
C [auth A], G [auth E]	IPR037534	Polymerase acidic protein	Family
C [auth A], G [auth E]	IPR038372	Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain	Homologous Superfamily
D [auth B], H [auth F]	IPR007099	RNA-directed RNA polymerase, negative-strand RNA virus	Domain
D [auth B], H [auth F]	IPR001407	Influenza RNA-dependent RNA polymerase subunit PB1	Family
E [auth C], I [auth G]	IPR001591	Influenza RNA-dependent RNA polymerase subunit PB2	Family
E [auth C], I [auth G]	IPR049106	Influenza RNA polymerase PB2, N-terminal region	Domain
E [auth C], I [auth G]	IPR049115	Influenza RNA polymerase PB2, C-terminal domain	Domain
E [auth C], I [auth G]	IPR049110	Influenza RNA polymerase PB2, second domain	Domain
E [auth C], I [auth G]	IPR049114	Influenza RNA polymerase PB2, sixth domain	Domain
E [auth C], I [auth G]	IPR049113	Polymerase basic protein 2, helical domain	Domain
E [auth C], I [auth G]	IPR049111	Influenza RNA polymerase PB2, middle domain	Domain
E [auth C], I [auth G]	IPR048298	Influenza RNA polymerase PB2, CAP binding domain	Domain
E [auth C], I [auth G]	IPR037258	PB2, C-terminal	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.