3L56

Crystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/viet nam/1203/2004 (h5n1)

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)
B	d3l56b2	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	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
B	d3l56b1	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	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
A	d3l56a2	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	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
A	d3l56a1	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	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Flu_PB2_6th	e3l56B2	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)
B	Flu_PB2_7th	e3l56B1	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)
A	Flu_PB2_6th	e3l56A1	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)
A	Flu_PB2_7th	e3l56A2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.30.90	Alpha Beta	2-Layer Sandwich	Defensin A-like	Polymerase Basic Protein 2, C-terminal domain	CATH (4.3.0)
A	3.30.30.90	Alpha Beta	2-Layer Sandwich	Defensin A-like	Polymerase Basic Protein 2, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	Polymerase PB2	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	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 symbiont-mediated perturbation of host cellular process 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 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 symbiont-mediated perturbation of host cellular process 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 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 symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway 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 modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001591	Influenza RNA-dependent RNA polymerase subunit PB2	Family
A, B	IPR049106	Influenza RNA polymerase PB2, N-terminal region	Domain
A, B	IPR049115	Influenza RNA polymerase PB2, C-terminal domain	Domain
A, B	IPR049110	Influenza RNA polymerase PB2, second domain	Domain
A, B	IPR049114	Influenza RNA polymerase PB2, sixth domain	Domain
A, B	IPR049113	Polymerase basic protein 2, helical domain	Domain
A, B	IPR049111	Influenza RNA polymerase PB2, middle domain	Domain
A, B	IPR048298	Influenza RNA polymerase PB2, CAP binding domain	Domain
A, B	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.