6OGZ | pdb_00006ogz

In situ structure of Rotavirus RNA-dependent RNA polymerase at transcript-elongated state

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth J]	SCOP2B Superfamily	Reovirus inner layer core protein p3	8097804	3001935	SCOP2B (2022-06-29)
J [auth K]	SCOP2B Superfamily	Reovirus inner layer core protein p3	8097804	3001935	SCOP2B (2022-06-29)
K [auth L]	SCOP2B Superfamily	Reovirus inner layer core protein p3	8097804	3001935	SCOP2B (2022-06-29)
M [auth N]	SCOP2B Superfamily	Reovirus inner layer core protein p3	8097804	3001935	SCOP2B (2022-06-29)
L [auth M]	SCOP2B Superfamily	Reovirus inner layer core protein p3	8097804	3001935	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Reovirus inner layer core protein p3	8097804	3001935	SCOP2B (2022-06-29)
G [auth I]	SCOP2B Superfamily	Reovirus inner layer core protein p3	8097804	3001935	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Reovirus inner layer core protein p3	8097804	3001935	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Reovirus inner layer core protein p3	8097804	3001935	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Reovirus inner layer core protein p3	8097804	3001935	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)
I [auth J]	Rota_VP2	e6ogzJ1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: Rota_VP2	ECOD (1.6)
J [auth K]	Rota_VP2	e6ogzK1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: Rota_VP2	ECOD (1.6)
K [auth L]	Rota_VP2	e6ogzL1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: Rota_VP2	ECOD (1.6)
M [auth N]	Rota_VP2	e6ogzN1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: Rota_VP2	ECOD (1.6)
L [auth M]	Rota_VP2	e6ogzM1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: Rota_VP2	ECOD (1.6)
H	Rota_VP2	e6ogzH1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: Rota_VP2	ECOD (1.6)
G [auth I]	Rota_VP2	e6ogzI1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: Rota_VP2	ECOD (1.6)
F [auth G]	Rota_VP2	e6ogzG1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: Rota_VP2	ECOD (1.6)
E [auth F]	Rota_VP2	e6ogzF1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: Rota_VP2	ECOD (1.6)
D [auth E]	Rota_VP2	e6ogzE1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: Rota_VP2	ECOD (1.6)
C [auth A]	EUF08094	e6ogzA4	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: EUF08094	ECOD (1.6)
C [auth A]	Rotavirus_VP1	e6ogzA2	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: Rotavirus_VP1	ECOD (1.6)
C [auth A]	RdRP_4_1st	e6ogzA3	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 additional helical subdomain in reovirus polymerase lambda3	F: RdRP_4_1st	ECOD (1.6)
C [auth A]	RdRP_4_2nd	e6ogzA1	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_4_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	1.20.120.1390	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (utative)
C [auth A]	1.10.10.1990	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Viral RNA-directed RNA polymerase, 4-helical domain	CATH (utative)
C [auth A]	3.30.70.2480	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
C [auth A]	1.10.357.80	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (utative)
C [auth A]	3.30.230.140	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
C [auth A]	1.20.120.1400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth E], E [auth F], F [auth G], G [auth I], H, D [auth E], E [auth F], F [auth G], G [auth I], H, I [auth J], J [auth K], K [auth L], L [auth M], M [auth N]	Inner capsid protein VP2	RNA binding binding nucleic acid binding	-	viral capsid icosahedral viral capsid virion component viral inner capsid viral nucleocapsid T=2 icosahedral viral capsid
C [auth A]	RNA-dependent RNA polymerase of rotavirus A	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 RNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide 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 RNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process viral genome replication viral process viral life cycle	virion component
B [auth C]	RNA (5'-R(PAPUPAPUPAPUPAPUPAPUPAPUPAPUPAPUP*A)-3')	-	-	-
A [auth B]	RNA (5'-R(PUPAPUPAPUPAPUPAPUPAPUPAPUPAPUPAPUPA)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E], E [auth F], F [auth G], G [auth I], H, D [auth E], E [auth F], F [auth G], G [auth I], H, I [auth J], J [auth K], K [auth L], L [auth M], M [auth N]	IPR007779	Rotavirus VP2	Family
C [auth A]	IPR001795	RNA-directed RNA polymerase, luteovirus	Family
C [auth A]	IPR007097	RNA-directed RNA polymerase, reovirus	Domain
C [auth A]	IPR042032	Viral RNA-directed RNA polymerase, 4-helical domain	Homologous Superfamily
C [auth A]	IPR022071	Rotavirus VP1 RNA-directed RNA polymerase, C-terminal	Domain
C [auth A]	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.