4A8Q

Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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	d4a8qa_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	dsRNA phage RNA-dependent RNA-polymerase	dsRNA phage RNA-dependent RNA-polymerase	(Cystovirus phi6 ) [TaxId: 10879 ],	SCOPe (2.08)
B	d4a8qb_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	dsRNA phage RNA-dependent RNA-polymerase	dsRNA phage RNA-dependent RNA-polymerase	(Cystovirus phi6 ) [TaxId: 10879 ],	SCOPe (2.08)
C	d4a8qc_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	dsRNA phage RNA-dependent RNA-polymerase	dsRNA phage RNA-dependent RNA-polymerase	(Cystovirus phi6 ) [TaxId: 10879 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033169	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033169	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033169	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033169	3001272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033169	3001272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033169	3001272	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00680	e4a8qA3	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: PF00680	ECOD (1.6)
A	PF00680	e4a8qA4	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: PF00680	ECOD (1.6)
B	PF00680	e4a8qB3	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: PF00680	ECOD (1.6)
B	PF00680	e4a8qB4	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: PF00680	ECOD (1.6)
C	PF00680	e4a8qC3	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: PF00680	ECOD (1.6)
C	PF00680	e4a8qC4	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: PF00680	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.490.60	Mainly Alpha	Orthogonal Bundle	Globin-like	Phage p2 RNA dependent RNA polymerase domain	CATH (4.3.0)
A	3.30.70.1600	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	6.20.410.10	Special	Other non-globular	Dihydrolipoamide Transferase		CATH (4.3.0)
B	1.10.490.60	Mainly Alpha	Orthogonal Bundle	Globin-like	Phage p2 RNA dependent RNA polymerase domain	CATH (4.3.0)
B	3.30.70.1600	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	6.20.410.10	Special	Other non-globular	Dihydrolipoamide Transferase		CATH (4.3.0)
C	1.10.490.60	Mainly Alpha	Orthogonal Bundle	Globin-like	Phage p2 RNA dependent RNA polymerase domain	CATH (4.3.0)
C	3.30.70.1600	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	6.20.410.20	Special	Other non-globular	Dihydrolipoamide Transferase		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00680	Viral RNA-dependent RNA polymerase (RdRP_1)	Viral RNA-dependent RNA polymerase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	RNA-DIRECTED RNA POLYMERASE	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 binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound 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 binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding uridylyltransferase activity RNA uridylyltransferase activity RNA binding nucleic acid binding cation binding ion binding metal ion 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 gene expression DNA-templated transcription	virion component
D [auth F], E [auth G], F [auth H]	5'-D(DTPTPCPGPCPGP)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR007096	RNA-directed RNA polymerase, catalytic domain, bacteriophage	Domain
A, B, C	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A, B, C	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C	IPR043110	Cystovirus, RNA-directed RNA polymerase, N-terminal	Homologous Superfamily
A, B, C	IPR016406	Cystovirus, RNA-directed RNA polymerase	Family

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.