6FHI

Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 19-mer serine 5 phosphorylated Pol II CTD peptide with a truncated linker.

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Flu_PB1_2nd	e6fhiB2	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	e6fhiB3	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	e6fhiB1	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)
C	Flu_PB2_6th	e6fhiC3	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	e6fhiC6	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	e6fhiC1	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	e6fhiC5	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	e6fhiC4	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	e6fhiC2	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	e6fhiC7	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)
A	Flu_PA_C	e6fhiA1	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	e6fhiA2	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)

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
B	PF00602	Influenza RNA-dependent RNA polymerase subunit PB1 (Flu_PB1)	Influenza RNA-dependent RNA polymerase subunit PB1	-	Family
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	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	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
A	PF00603	Influenza RNA-dependent RNA polymerase subunit PA (Flu_PA)	Influenza RNA-dependent RNA polymerase subunit PA	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	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	symbiont-mediated suppression of host transcription 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 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 symbiont-mediated suppression of host transcription 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 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	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus host intracellular organelle intracellular anatomical structure cytoplasm host cell cytoplasm
C	Polymerase basic protein 2	RNA binding binding organic cyclic compound binding nucleic acid binding	symbiont-mediated suppression of host transcription 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 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 7-methylguanosine mRNA capping symbiont-mediated suppression of host transcription 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 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 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 cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell mitochondrion host cell cytoplasm part host intracellular organelle host cell nucleus virion component
E [auth V]	RNA (5'-R(PAPGPUPAPGPUPAPAPCPAPAPGPAPGPGPG)-3')	-	-	-
F [auth X]	TYR-SER-PRO-THR-SEP-PRO-SER-TYR-SER-PRO-SER-TYR-SER-PRO-THR-SEP-PRO-SER-TYR	-	-	-
A	Polymerase acidic protein	RNA binding binding organic cyclic compound 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	-
D [auth R]	RNA (5'-R(UPAPUPAPCPCPUPCPUPGPCPUP*U)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
A	IPR001009	Influenza RNA-dependent RNA polymerase subunit PA	Family
A	IPR038372	Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain	Homologous Superfamily

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.