3ZED | pdb_00003zed

X-ray structure of the birnavirus VP1-VP3 complex

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)
A	d3zeda_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	automated matches	automated matches	(Infectious pancreatic necrosis virus ) [TaxId: 11002 ],	SCOPe (2.08)
B	d3zedb_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	automated matches	automated matches	(Infectious pancreatic necrosis virus ) [TaxId: 11002 ],	SCOPe (2.08)
C	d3zedc_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	automated matches	automated matches	(Infectious pancreatic necrosis virus ) [TaxId: 11002 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Birna_RdRp_2nd	e3zedA2	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: Birna_RdRp_2nd	ECOD (1.6)
A	Birna_RdRp_3rd	e3zedA3	A: alpha complex topology	X: Sigma2 domain-like	H: C-terminal bundle domain in birnaviruse RNA-dependent RNA polymerase (From Topology)	T: C-terminal bundle domain in birnaviruse RNA-dependent RNA polymerase	F: Birna_RdRp_3rd	ECOD (1.6)
A	Birna_RdRp_1st	e3zedA1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: 'palm' domain in birnaviruse RNA-dependent RNA polymerase	F: Birna_RdRp_1st	ECOD (1.6)
B	Birna_RdRp_2nd	e3zedB3	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: Birna_RdRp_2nd	ECOD (1.6)
B	Birna_RdRp_3rd	e3zedB1	A: alpha complex topology	X: Sigma2 domain-like	H: C-terminal bundle domain in birnaviruse RNA-dependent RNA polymerase (From Topology)	T: C-terminal bundle domain in birnaviruse RNA-dependent RNA polymerase	F: Birna_RdRp_3rd	ECOD (1.6)
B	Birna_RdRp_1st	e3zedB2	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: 'palm' domain in birnaviruse RNA-dependent RNA polymerase	F: Birna_RdRp_1st	ECOD (1.6)
C	Birna_RdRp_2nd	e3zedC1	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: Birna_RdRp_2nd	ECOD (1.6)
C	Birna_RdRp_3rd	e3zedC3	A: alpha complex topology	X: Sigma2 domain-like	H: C-terminal bundle domain in birnaviruse RNA-dependent RNA polymerase (From Topology)	T: C-terminal bundle domain in birnaviruse RNA-dependent RNA polymerase	F: Birna_RdRp_3rd	ECOD (1.6)
C	Birna_RdRp_1st	e3zedC2	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: 'palm' domain in birnaviruse RNA-dependent RNA polymerase	F: Birna_RdRp_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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, E, F	CAPSID PROTEIN VP3	structural molecule activity peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid T=13 icosahedral viral capsid 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, E, F	IPR029053	Viral coat protein subunit	Homologous Superfamily
D, E, F	IPR043048	Birnavirus VP3, domain 1	Homologous Superfamily
D, E, F	IPR002662	Birnavirus VP2 protein	Family
D, E, F	IPR025775	Birnavirus VP4 protease domain	Domain
D, E, F	IPR002663	Birnavirus VP3 protein	Family
D, E, F	IPR043049	Birnavirus VP3, domain 2	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.