2YIB | pdb_00002yib

Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D		e2yibD1	A: Single-stranded left-handed beta-helix	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: JmjC_2	F:	ECOD (20:10:01)
C		e2yibC1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: Internalin_N	F:	ECOD (20:10:01)
B		e2yibB1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: Internalin_N	F:	ECOD (20:10:01)
A		e2yibA1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: Internalin_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.1730.10	Alpha Beta	Alpha-Beta Complex	Infectious bursal virus vp1 polymerase fold	Infectious bursal virus vp1 polymerase domain	CATH (4.3.0)
D	1.10.287.540	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
D	6.10.140.300	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C	3.90.1730.10	Alpha Beta	Alpha-Beta Complex	Infectious bursal virus vp1 polymerase fold	Infectious bursal virus vp1 polymerase domain	CATH (4.3.0)
C	1.10.287.540	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
C	6.10.140.300	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C	1.20.1270.270	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
B	3.90.1730.10	Alpha Beta	Alpha-Beta Complex	Infectious bursal virus vp1 polymerase fold	Infectious bursal virus vp1 polymerase domain	CATH (4.3.0)
B	1.10.287.540	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
B	6.10.140.300	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	1.20.1270.270	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
A	3.90.1730.10	Alpha Beta	Alpha-Beta Complex	Infectious bursal virus vp1 polymerase fold	Infectious bursal virus vp1 polymerase domain	CATH (4.3.0)
A	1.10.287.540	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
A	6.10.140.300	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	1.20.1270.270	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF20488	Birnavirus RNA dependent RNA polymerase (VP1), thumb domain (Birna_VP1_thumb)	Birnavirus RNA dependent RNA polymerase (VP1), thumb domain	Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteristic permuted order, thus, it adopts a ...	Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteristic permuted order, thus, it adopts a unique active site topology [2,3]. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps [1,2,3]. This entry covers the thumb domain of RdRP from Birnaviruses.	Domain
A, B, C	PF20488	Birnavirus RNA dependent RNA polymerase (VP1), thumb domain (Birna_VP1_thumb)	Birnavirus RNA dependent RNA polymerase (VP1), thumb domain	Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteristic permuted order, thus, it adopts a ...	Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteristic permuted order, thus, it adopts a unique active site topology [2,3]. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps [1,2,3]. This entry covers the thumb domain of RdRP from Birnaviruses.	Domain
A, B, C	PF20489	Birnavirus RNA dependent RNA polymerase (VP1), C-terminal (Birna_RdRp_C)	Birnavirus RNA dependent RNA polymerase (VP1), C-terminal	Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all clas ...	Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps [1]. This RdRp has the five essential RNA polymerase motifs in a permuted order of C-A-B-D-E to form a conserved catalytic active site [2,3]. This domain is mostly alpha-helical that runs across the canyon in the front of the palm, and wraps around the fingers subdomain [2], which may function to prevent back-primed RNA synthesis during protein priming.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	RNA-DIRECTED RNA POLYMERASE	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 guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide 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 guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	viral genome replication viral process viral life cycle	virion component
A, B, C	RNA-DIRECTED RNA POLYMERASE	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 guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide 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 guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	viral genome replication viral process viral life cycle	virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR046750	RNA-directed RNA polymerase, C-terminal, birnavirus	Domain
D	IPR046812	RNA-directed RNA polymerase, palm domain superfamily, Birnavirus	Homologous Superfamily
D	IPR007100	Birnavirus RNA-directed RNA polymerase, palm domain	Domain
D	IPR046752	RNA-directed RNA polymerase, thumb domain, birnavirus	Domain
D	IPR046813	RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus	Homologous Superfamily
D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C	IPR046750	RNA-directed RNA polymerase, C-terminal, birnavirus	Domain
A, B, C	IPR046812	RNA-directed RNA polymerase, palm domain superfamily, Birnavirus	Homologous Superfamily
A, B, C	IPR007100	Birnavirus RNA-directed RNA polymerase, palm domain	Domain
A, B, C	IPR046752	RNA-directed RNA polymerase, thumb domain, birnavirus	Domain
A, B, C	IPR046813	RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus	Homologous Superfamily
A, B, C	IPR043502	DNA/RNA polymerase superfamily	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.