5Y3D | pdb_00005y3d

Structural insight into the interaction between RNA polymerase and VPg for norovirus replication

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d5y3da_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
B	d5y3db_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
C	d5y3dc_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
D	d5y3dd_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
E	d5y3de_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
F	d5y3df_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	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	RdRP_1_C	e5y3dA2	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: RdRP_1_C	ECOD (1.6)
A	RdRP_1_N	e5y3dA1	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: RdRP_1_N	ECOD (1.6)
B	RdRP_1_C	e5y3dB1	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: RdRP_1_C	ECOD (1.6)
B	RdRP_1_N	e5y3dB2	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: RdRP_1_N	ECOD (1.6)
C	RdRP_1_C	e5y3dC2	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: RdRP_1_C	ECOD (1.6)
C	RdRP_1_N	e5y3dC1	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: RdRP_1_N	ECOD (1.6)
D	RdRP_1_C	e5y3dD1	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: RdRP_1_C	ECOD (1.6)
D	RdRP_1_N	e5y3dD2	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: RdRP_1_N	ECOD (1.6)
E	RdRP_1_C	e5y3dE1	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: RdRP_1_C	ECOD (1.6)
E	RdRP_1_N	e5y3dE2	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: RdRP_1_N	ECOD (1.6)
F	RdRP_1_C	e5y3dF1	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: RdRP_1_C	ECOD (1.6)
F	RdRP_1_N	e5y3dF2	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: RdRP_1_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.10.250.3230	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
A	1.20.960.20	Mainly Alpha	Up-down Bundle	Mitochondrial Import Receptor Subunit Tom20	Chain A	CATH (utative)
B	6.10.250.3230	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
B	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
B	1.20.960.20	Mainly Alpha	Up-down Bundle	Mitochondrial Import Receptor Subunit Tom20	Chain A	CATH (utative)
C	6.10.250.3230	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
C	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
C	1.20.960.20	Mainly Alpha	Up-down Bundle	Mitochondrial Import Receptor Subunit Tom20	Chain A	CATH (utative)
D	6.10.250.3230	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
D	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
D	1.20.960.20	Mainly Alpha	Up-down Bundle	Mitochondrial Import Receptor Subunit Tom20	Chain A	CATH (utative)
E	6.10.250.3230	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
E	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
E	1.20.960.20	Mainly Alpha	Up-down Bundle	Mitochondrial Import Receptor Subunit Tom20	Chain A	CATH (utative)
F	6.10.250.3230	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
F	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
F	1.20.960.20	Mainly Alpha	Up-down Bundle	Mitochondrial Import Receptor Subunit Tom20	Chain A	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H	viral protein genome-linked (VPg)	-	-	-
A, B, C, D, E A, B, C, D, E, F	RNA-dependent RNA polymerase	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity 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 cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity 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 transferase activity, transferring phosphorus-containing groups RNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity cation binding metal ion binding	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 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 gene expression DNA-templated transcription proteolysis protein metabolic process	cellular anatomical structure membrane host cellular component host intracellular part host cell perinuclear region of cytoplasm host cell cytoplasm host cell part host intracellular region other organism part host cell cytoplasm part extracellular region host intracellular membrane-bounded organelle host cell membrane host intracellular organelle cellular anatomical structure membrane host cellular component host intracellular part host cell perinuclear region of cytoplasm host cell cytoplasm host cell part host intracellular region other organism part host cell cytoplasm part extracellular region host intracellular membrane-bounded organelle host cell membrane host intracellular organelle host cell endosome membrane host cell endosome host cell mitochondrion host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001665	Norovirus peptidase C37	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR014759	Helicase, superfamily 3, single-stranded RNA virus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR013614	Viral polyprotein, Caliciviridae N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000605	Helicase, superfamily 3, single-stranded DNA/RNA virus	Domain

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.