Annotations: 4GDF

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8042358	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8041337	3001937	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8042358	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8041337	3001937	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8041337	3001937	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8042358	3002019	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8042358	3002019	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8041337	3001937	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)
A	Polyoma_lg_T_C	e4gdfA4	A: alpha arrays	X: N-terminal domain of large tumor antigen (From Topology)	H: N-terminal domain of large tumor antigen (From Topology)	T: N-terminal domain of large tumor antigen	F: Polyoma_lg_T_C	ECOD (1.6)
A	Polyoma_lg_T_C	e4gdfA5	A: alpha complex topology	X: PriB N-terminal domain-like (From Topology)	H: PriB N-terminal domain-like (From Topology)	T: PriB N-terminal domain-like	F: Polyoma_lg_T_C	ECOD (1.6)
A	T_Ag_DNA_bind	e4gdfA2	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: T_Ag_DNA_bind	ECOD (1.6)
A	Polyoma_lg_T_C	e4gdfA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Polyoma_lg_T_C	ECOD (1.6)
B	Polyoma_lg_T_C	e4gdfB3	A: alpha arrays	X: N-terminal domain of large tumor antigen (From Topology)	H: N-terminal domain of large tumor antigen (From Topology)	T: N-terminal domain of large tumor antigen	F: Polyoma_lg_T_C	ECOD (1.6)
B	Polyoma_lg_T_C	e4gdfB4	A: alpha complex topology	X: PriB N-terminal domain-like (From Topology)	H: PriB N-terminal domain-like (From Topology)	T: PriB N-terminal domain-like	F: Polyoma_lg_T_C	ECOD (1.6)
B	T_Ag_DNA_bind	e4gdfB1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: T_Ag_DNA_bind	ECOD (1.6)
B	Polyoma_lg_T_C	e4gdfB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Polyoma_lg_T_C	ECOD (1.6)
E	Polyoma_lg_T_C	e4gdfE3	A: alpha arrays	X: N-terminal domain of large tumor antigen (From Topology)	H: N-terminal domain of large tumor antigen (From Topology)	T: N-terminal domain of large tumor antigen	F: Polyoma_lg_T_C	ECOD (1.6)
E	Polyoma_lg_T_C	e4gdfE4	A: alpha complex topology	X: PriB N-terminal domain-like (From Topology)	H: PriB N-terminal domain-like (From Topology)	T: PriB N-terminal domain-like	F: Polyoma_lg_T_C	ECOD (1.6)
E	T_Ag_DNA_bind	e4gdfE1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: T_Ag_DNA_bind	ECOD (1.6)
E	Polyoma_lg_T_C	e4gdfE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Polyoma_lg_T_C	ECOD (1.6)
F	Polyoma_lg_T_C	e4gdfF3	A: alpha arrays	X: N-terminal domain of large tumor antigen (From Topology)	H: N-terminal domain of large tumor antigen (From Topology)	T: N-terminal domain of large tumor antigen	F: Polyoma_lg_T_C	ECOD (1.6)
F	Polyoma_lg_T_C	e4gdfF4	A: alpha complex topology	X: PriB N-terminal domain-like (From Topology)	H: PriB N-terminal domain-like (From Topology)	T: PriB N-terminal domain-like	F: Polyoma_lg_T_C	ECOD (1.6)
F	T_Ag_DNA_bind	e4gdfF1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: T_Ag_DNA_bind	ECOD (1.6)
F	Polyoma_lg_T_C	e4gdfF2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Polyoma_lg_T_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
A	1.10.10.510	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Zinc finger, large T-antigen D1 domain	CATH (4.3.0)
A	1.20.1050.70	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
B	1.10.10.510	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Zinc finger, large T-antigen D1 domain	CATH (4.3.0)
B	1.20.1050.70	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
E	1.10.10.510	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Zinc finger, large T-antigen D1 domain	CATH (4.3.0)
E	1.20.1050.70	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
F	1.10.10.510	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Zinc finger, large T-antigen D1 domain	CATH (4.3.0)
F	1.20.1050.70	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E, F	PF02217	Origin of replication binding protein (T_Ag_DNA_bind)	Origin of replication binding protein	This domain of large T antigen binds to the SV40 origin of DNA replication [1].	Domain
A, B, E, F	PF06431	Polyomavirus large T antigen C-terminus (Polyoma_lg_T_C)	Polyomavirus large T antigen C-terminus	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, E, F	Large T antigen	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding DNA replication origin binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity hydrolase activity adenyl ribonucleotide binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding DNA replication origin binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity hydrolase activity 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 cation binding metal ion binding identical protein binding protein binding single-stranded DNA binding	cellular biosynthetic process cellular metabolic process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process viral genome replication cellular biosynthetic process cellular metabolic process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process viral genome replication organic cyclic compound biosynthetic process organic substance biosynthetic process viral process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host JAK-STAT cascade biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway modulation by symbiont of host process symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host cell cycle progression symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint bidirectional double-stranded viral DNA replication symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated perturbation of host ubiquitin-like protein modification DNA duplex unwinding DNA-templated DNA replication DNA geometric change chromosome organization DNA conformation change DNA unwinding involved in DNA replication cellular component organization organelle organization DNA replication cellular component organization or biogenesis	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell part host intracellular region cellular anatomical entity host cell nucleus host intracellular organelle
C, G	DNA (32-MER)	-	-	-
D, H	DNA (32-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E, F	IPR001623	DnaJ domain	Domain
A, B, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, E, F	IPR017910	Zinc finger, large T-antigen D1-type	Domain
A, B, E, F	IPR003133	T antigen, Ori-binding	Domain
A, B, E, F	IPR037102	Zinc finger, large T-antigen D1 domain superfamily	Homologous Superfamily
A, B, E, F	IPR036869	Chaperone J-domain superfamily	Homologous Superfamily
A, B, E, F	IPR014015	Helicase, superfamily 3, DNA virus	Domain
A, B, E, F	IPR016392	Large T antigen, polyomaviridae	Family
A, B, E, F	IPR010932	Large T antigen, polyomavirus, C-terminal	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.