5M3J | pdb_00005m3j

Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD

External Resource: Annotation

Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Flu_PB2_6th	e5m3jC7	A: alpha arrays	X: PB2 '627' domain-related (From Homology)	H: PB2 '627' domain-related	T: Polymerase basic protein 2 (PB2) '627' domain	F: Flu_PB2_6th	ECOD (1.6)
C	Flu_PB2_4th	e5m3jC2	A: alpha arrays	X: Helical domain in PB2 (From Topology)	H: Helical domain in PB2 (From Topology)	T: Helical domain in PB2	F: Flu_PB2_4th	ECOD (1.6)
C	Flu_PB2_7th	e5m3jC4	A: a+b two layers	X: PB2 C-terminal domain-like (From Topology)	H: PB2 C-terminal domain-like (From Topology)	T: PB2 C-terminal domain-like	F: Flu_PB2_7th	ECOD (1.6)
C	Flu_PB2_2nd	e5m3jC3	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: Flu_PB2_2nd	ECOD (1.6)
C	Flu_PB2_5th	e5m3jC1	A: a+b three layers	X: Polymerase basic protein 2 cap-binding domain (From Topology)	H: Polymerase basic protein 2 cap-binding domain (From Topology)	T: Polymerase basic protein 2 cap-binding domain	F: Flu_PB2_5th	ECOD (1.6)
C	Flu_PB2_3rd	e5m3jC5	A: a+b complex topology	X: Middle domain in PB2 (From Topology)	H: Middle domain in PB2 (From Topology)	T: Middle domain in PB2	F: Flu_PB2_3rd	ECOD (1.6)
C	Flu_PB2_1st	e5m3jC6	A: extended segments	X: RNA polymerase PB2 N-terminal fragment (From Topology)	H: RNA polymerase PB2 N-terminal fragment (From Topology)	T: RNA polymerase PB2 N-terminal fragment	F: Flu_PB2_1st	ECOD (1.6)
B	Flu_PB1_2nd	e5m3jB1	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: Flu_PB1_2nd	ECOD (1.6)
B	Flu_PB1_1st	e5m3jB2	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: Flu_PB1_1st	ECOD (1.6)
B	Flu_PB1_3rd	e5m3jB3	A: extended segments	X: RNA polymerase PB1 C-terminal fragment (From Topology)	H: RNA polymerase PB1 C-terminal fragment (From Topology)	T: RNA polymerase PB1 C-terminal fragment	F: Flu_PB1_3rd	ECOD (1.6)
A	Flu_PA_C	e5m3jA1	A: a+b complex topology	X: Polymerase acidic protein (From Topology)	H: Polymerase acidic protein (From Topology)	T: Polymerase acidic protein	F: Flu_PA_C	ECOD (1.6)
A	Flu_PA_N	e5m3jA2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Flu_PA_N	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth X]	DNA-directed RNA polymerase 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 hydrolase activity extracellular matrix binding binding microfibril binding RNA 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 hydrolase activity extracellular matrix binding binding microfibril binding RNA binding nucleic acid binding chromatin binding promoter-specific chromatin binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding DNA binding protein binding kinase binding enzyme binding DNA-directed RNA polymerase activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding transition metal ion binding zinc ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process DNA-templated transcription termination regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process RNA processing positive regulation of cellular process regulation of biosynthetic process RNA splicing regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of RNA splicing regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of RNA splicing regulation of metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm RNA polymerase II, core complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen membraneless organelle intracellular membraneless organelle chromosome
E [auth V]	RNA (5'-R(PAPGPUPAPGPUPAPAPCPAPAPGPAPG)-3')	-	-	-
D [auth R]	RNA (5'-R(UPAPUPAPCPCPUPCPUPGPCPUPUPC)-3')	-	-	-
C	Polymerase basic protein 2	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	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 cap snatching negative stranded viral RNA transcription viral transcription RNA-templated viral transcription symbiont-mediated suppression of host gene expression 7-methylguanosine mRNA capping 7-methylguanosine RNA capping RNA capping gene expression mRNA processing mRNA metabolic process RNA 5'-end processing RNA processing 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
B	RNA-directed RNA polymerase catalytic subunit	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule 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 binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule 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 nucleic acid binding cation binding ion 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 gene expression DNA-templated transcription	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
A	Polymerase acidic protein	hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule 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 cap snatching negative stranded viral RNA transcription viral transcription RNA-templated viral transcription symbiont-mediated suppression of host gene expression viral translational frameshifting viral translation gene expression DNA-templated transcription	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth X]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
F [auth X]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
F [auth X]	IPR007075	RNA polymerase Rpb1, domain 6	Domain
F [auth X]	IPR000684	RNA polymerase II, heptapeptide repeat, eukaryotic	Repeat
F [auth X]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
F [auth X]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
F [auth X]	IPR006592	RNA polymerase, N-terminal	Domain
F [auth X]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
F [auth X]	IPR007073	RNA polymerase Rpb1, domain 7	Domain
F [auth X]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
F [auth X]	IPR038593	RNA polymerase Rpb1, domain 7 superfamily	Homologous Superfamily
F [auth X]	IPR000722	RNA polymerase, alpha subunit	Domain
F [auth X]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
F [auth X]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
C	IPR001591	Influenza RNA-dependent RNA polymerase subunit PB2	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
B	IPR007099	RNA-directed RNA polymerase, negative-strand RNA virus	Domain
B	IPR001407	Influenza RNA-dependent RNA polymerase subunit PB1	Family
A	IPR001009	Influenza RNA-dependent RNA polymerase subunit PA	Family
A	IPR037534	Polymerase acidic protein	Family
A	IPR038372	Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
F [auth X]	Pharos: P24928	acute myeloid leukemia central nervous system cancer metabolic syndrome X astrocytic tumor diabetes mellitus osteosarcoma atrial fibrillation IgA glomerulonephritis uterine corpus leiomyoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
F [auth X]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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.

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