5A22

Structure of the L protein of vesicular stomatitis virus from electron cryomicroscopy

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
A	Mononeg_RNA_pol_3rd	e5a22A3	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: Mononeg_RNA_pol_3rd	ECOD (1.6)
A	Methyltrans_Mon_1st	e5a22A5	A: alpha bundles	X: Vesicular stomatitis virus L polymerase connector domain (From Topology)	H: Vesicular stomatitis virus L polymerase connector domain (From Topology)	T: Vesicular stomatitis virus L polymerase connector domain	F: Methyltrans_Mon_1st	ECOD (1.6)
A	Mononeg_mRNAcap	e5a22A4	A: alpha complex topology	X: C-terminal additional helical subdomain in reovirus polymerase lambda3 (From Topology)	H: C-terminal additional helical subdomain in reovirus polymerase lambda3 (From Topology)	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F: Mononeg_mRNAcap	ECOD (1.6)
A	Mononeg_RNA_pol_1st	e5a22A1	A: alpha complex topology	X: N-terminal additional helical subdomain in reovirus polymerase lambda3 (From Homology)	H: N-terminal additional helical subdomain in reovirus polymerase lambda3	T: N-terminal domain in vesicular stomatitis virus RNA polymerase L	F: Mononeg_RNA_pol_1st	ECOD (1.6)
A	Methyltrans_Mon_3rd	e5a22A7	A: alpha complex topology	X: Vesicular stomatitis virus L polymerase C-terminal domain (From Topology)	H: Vesicular stomatitis virus L polymerase C-terminal domain (From Topology)	T: Vesicular stomatitis virus L polymerase C-terminal domain	F: Methyltrans_Mon_3rd	ECOD (1.6)
A	Mononeg_RNA_pol_2nd	e5a22A2	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: Mononeg_RNA_pol_2nd	ECOD (1.6)
A	Methyltrans_Mon_2nd	e5a22A6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltrans_Mon_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14318	Mononegavirales mRNA-capping region V (Mononeg_mRNAcap)	Mononegavirales mRNA-capping region V	This V domain of L RNA-polymerase carries a new motif, GxxTx(n)HR, that is essential for mRNA cap formation. Nonsegmented negative-sense (NNS) RNA viruses, Mononegavirales, cap their mRNA by an unconventional mechanism. Specifically, 5'-monophosphate ...	This V domain of L RNA-polymerase carries a new motif, GxxTx(n)HR, that is essential for mRNA cap formation. Nonsegmented negative-sense (NNS) RNA viruses, Mononegavirales, cap their mRNA by an unconventional mechanism. Specifically, 5'-monophosphate mRNA is transferred to GDP derived from GTP through a reaction that involves a covalent intermediate between the large polymerase protein L and mRNA. The V region is essential for this process [1].	Domain
A	PF00946	Mononegavirales RNA dependent RNA polymerase (Mononeg_RNA_pol)	Mononegavirales RNA dependent RNA polymerase	-	Family
A	PF21081	Virus-capping methyltransferase, C-terminal (Methyltrans_Mon_3rd)	Virus-capping methyltransferase, C-terminal	This is the C-terminal domain of the Mononegavirales single-stranded RNA viral RNA polymerase enzymes. This region, together with the connector domain (CD), flanks the methyltransferase domain (MT) and is likely involved in the structural rearrangeme ...	This is the C-terminal domain of the Mononegavirales single-stranded RNA viral RNA polymerase enzymes. This region, together with the connector domain (CD), flanks the methyltransferase domain (MT) and is likely involved in the structural rearrangements that appear to coordinate the enzymatic activities during transcription and replication [2,3].	Domain
A	PF14314	Virus-capping methyltransferase, MT domain (Methyltrans_Mon_2nd)	Virus-capping methyltransferase, MT domain	This is the methyltransferase region of the Mononegavirales single-stranded RNA viral RNA polymerase enzymes (L proteins). This region is involved in the mRNA-capping of the virion particles [1-3].	Domain
A	PF21080	Virus-capping methyltransferase, connector domain (Methyltrans_Mon_1st)	Virus-capping methyltransferase, connector domain	This is the connector domain (CD) from Mononegavirales single-stranded RNA viral RNA polymerase enzymes (L proteins). This domain flanks the methyltransferase domain (MT, Pfam:PF14314) and together with the C-terminal domain (CTD), in conjunction wit ...	This is the connector domain (CD) from Mononegavirales single-stranded RNA viral RNA polymerase enzymes (L proteins). This domain flanks the methyltransferase domain (MT, Pfam:PF14314) and together with the C-terminal domain (CTD), in conjunction with its phosphoprotein cofactor, likely facilitates the structural rearrangements that appear to coordinate the enzymatic activities during transcription and replication [2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	VESICULAR STOMATITIS VIRUS L POLYMERASE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule 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 methyltransferase activity transferase activity, transferring one-carbon groups S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity cation binding metal ion binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	viral gene expression viral process viral transcription cellular biosynthetic process RNA metabolic process viral life cycle RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral RNA genome replication organic substance biosynthetic process cellular metabolic process primary metabolic process viral gene expression viral process viral transcription cellular biosynthetic process RNA metabolic process viral life cycle RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral RNA genome replication organic substance biosynthetic process cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process negative stranded viral RNA replication viral genome replication biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process	virion component host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR014023	Mononegavirales RNA-directed RNA polymerase catalytic domain	Domain
A	IPR025786	Mononegavirus L protein 2-O-ribose methyltransferase	Domain
A	IPR017234	RNA-directed RNA polymerase, rhabdovirus	Family
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR026890	Mononegavirales mRNA-capping domain V	Domain
A	IPR039736	RNA-directed RNA polymerase L, C-terminal	Domain
A	IPR048397	Virus-capping methyltransferase, connector domain	Domain
A	IPR048398	Virus-capping methyltransferase, C-terminal domain	Domain
A	IPR039530	RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus	Domain

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.