1TUE

The X-ray Structure of the Papillomavirus Helicase in Complex with its Molecular Matchmaker E2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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	d1tuea1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication protein E1 helicase domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
A	d1tuea2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
C [auth D]	d1tued_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication protein E1 helicase domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
G [auth H]	d1tueh_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication protein E1 helicase domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
I [auth K]	d1tuek_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication protein E1 helicase domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
K [auth M]	d1tuem_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication protein E1 helicase domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
E [auth F]	d1tuef_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Replication protein E1 helicase domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
B	d1tueb1	All beta proteins	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
B	d1tueb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
D [auth E]	d1tuee_	All beta proteins	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
F [auth G]	d1tueg_	All beta proteins	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
H [auth J]	d1tuej_	All beta proteins	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
J [auth L]	d1tuel_	All beta proteins	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)
L [auth Q]	d1tueq_	All beta proteins	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	E2 regulatory, transactivation domain	(human papillomavirus 18 ) [TaxId: 333761 ],	SCOPe (2.08)

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	8040441	3002019	SCOP2B (2022-06-29)
C [auth D]	SCOP2 Family	Extended AAA-ATPase domain	8028062	4000283	SCOP2 (2022-06-29)
C [auth D]	SCOP2 Superfamily	RecA-like P-loop NTPases	8040441	3002019	SCOP2 (2022-06-29)
G [auth H]	SCOP2B Superfamily	RecA-like P-loop NTPases	8040441	3002019	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	RecA-like P-loop NTPases	8040441	3002019	SCOP2B (2022-06-29)
K [auth M]	SCOP2B Superfamily	RecA-like P-loop NTPases	8040441	3002019	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	RecA-like P-loop NTPases	8040441	3002019	SCOP2B (2022-06-29)
B	SCOP2 Family	E2 regulatory transactivation domain	8028061	4003014	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	E2 regulatory transactivation domain	8040440	3002015	SCOP2 (2022-06-29)
D [auth E]	SCOP2B Superfamily	E2 regulatory transactivation domain	8040440	3002015	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	E2 regulatory transactivation domain	8040440	3002015	SCOP2B (2022-06-29)
H [auth J]	SCOP2B Superfamily	E2 regulatory transactivation domain	8040440	3002015	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	E2 regulatory transactivation domain	8040440	3002015	SCOP2B (2022-06-29)
L [auth Q]	SCOP2B Superfamily	E2 regulatory transactivation domain	8040440	3002015	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	Parvo_NS1	e1tueA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Parvo_NS1	ECOD (1.6)
C [auth D]	Polyoma_lg_T_C	e1tueD1	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)
G [auth H]	Polyoma_lg_T_C	e1tueH1	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)
I [auth K]	Polyoma_lg_T_C	e1tueK1	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)
K [auth M]	Polyoma_lg_T_C	e1tueM1	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 [auth F]	Polyoma_lg_T_C	e1tueF1	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	PPV_E2_N_C,PPV_E2_N_N	e1tueB1	A: beta sandwiches	X: E2 regulatory, transactivation domain (From Topology)	H: E2 regulatory, transactivation domain (From Topology)	T: E2 regulatory, transactivation domain	F: PPV_E2_N_C,PPV_E2_N_N	ECOD (1.6)
D [auth E]	PPV_E2_N_C,PPV_E2_N_N	e1tueE1	A: beta sandwiches	X: E2 regulatory, transactivation domain (From Topology)	H: E2 regulatory, transactivation domain (From Topology)	T: E2 regulatory, transactivation domain	F: PPV_E2_N_C,PPV_E2_N_N	ECOD (1.6)
F [auth G]	PPV_E2_N_C,PPV_E2_N_N	e1tueG1	A: beta sandwiches	X: E2 regulatory, transactivation domain (From Topology)	H: E2 regulatory, transactivation domain (From Topology)	T: E2 regulatory, transactivation domain	F: PPV_E2_N_C,PPV_E2_N_N	ECOD (1.6)
H [auth J]	PPV_E2_N_C,PPV_E2_N_N	e1tueJ1	A: beta sandwiches	X: E2 regulatory, transactivation domain (From Topology)	H: E2 regulatory, transactivation domain (From Topology)	T: E2 regulatory, transactivation domain	F: PPV_E2_N_C,PPV_E2_N_N	ECOD (1.6)
J [auth L]	PPV_E2_N_C,PPV_E2_N_N	e1tueL1	A: beta sandwiches	X: E2 regulatory, transactivation domain (From Topology)	H: E2 regulatory, transactivation domain (From Topology)	T: E2 regulatory, transactivation domain	F: PPV_E2_N_C,PPV_E2_N_N	ECOD (1.6)
L [auth Q]	PPV_E2_N_C,PPV_E2_N_N	e1tueQ1	A: beta sandwiches	X: E2 regulatory, transactivation domain (From Topology)	H: E2 regulatory, transactivation domain (From Topology)	T: E2 regulatory, transactivation domain	F: PPV_E2_N_C,PPV_E2_N_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C [auth D]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G [auth H]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
I [auth K]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
K [auth M]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E [auth F]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.287.30	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	E2 (early) protein, N terminal domain, subdomain 1	CATH (4.3.0)
B	2.170.200.10	Mainly Beta	Beta Complex	Regulatory Protein E2	Chain: A	CATH (4.3.0)
D [auth E]	1.10.287.30	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	E2 (early) protein, N terminal domain, subdomain 1	CATH (4.3.0)
D [auth E]	2.170.200.10	Mainly Beta	Beta Complex	Regulatory Protein E2	Chain: A	CATH (4.3.0)
F [auth G]	1.10.287.30	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	E2 (early) protein, N terminal domain, subdomain 1	CATH (4.3.0)
F [auth G]	2.170.200.10	Mainly Beta	Beta Complex	Regulatory Protein E2	Chain: A	CATH (4.3.0)
H [auth J]	1.10.287.30	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	E2 (early) protein, N terminal domain, subdomain 1	CATH (4.3.0)
H [auth J]	2.170.200.10	Mainly Beta	Beta Complex	Regulatory Protein E2	Chain: A	CATH (4.3.0)
J [auth L]	1.10.287.30	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	E2 (early) protein, N terminal domain, subdomain 1	CATH (4.3.0)
J [auth L]	2.170.200.10	Mainly Beta	Beta Complex	Regulatory Protein E2	Chain: A	CATH (4.3.0)
L [auth Q]	1.10.287.30	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	E2 (early) protein, N terminal domain, subdomain 1	CATH (4.3.0)
L [auth Q]	2.170.200.10	Mainly Beta	Beta Complex	Regulatory Protein E2	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D], E [auth F], G [auth H], I [auth K], A, C [auth D], E [auth F], G [auth H], I [auth K], K [auth M]	PF00519	Papillomavirus helicase (PPV_E1_C)	Papillomavirus helicase	This is the C-terminal ATPase/helicase domain of Papillomavirus E1 protein, a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein Pfam:PF00508 [1,2]. The domain architecture of E1 is ...	This is the C-terminal ATPase/helicase domain of Papillomavirus E1 protein, a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein Pfam:PF00508 [1,2]. The domain architecture of E1 is similar to that of the SV40 T-antigen [1].	Domain
B, D [auth E], F [auth G], H [auth J], J [auth L], B, D [auth E], F [auth G], H [auth J], J [auth L], L [auth Q]	PF00508	E2 (early) protein, N terminal (PPV_E2_N)	E2 (early) protein, N terminal	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth D], E [auth F], G [auth H], I [auth K], A, C [auth D], E [auth F], G [auth H], I [auth K], K [auth M]	Replication protein E1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral genome replication viral process viral life cycle	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 host cell cytoplasm
B, D [auth E], F [auth G], H [auth J], J [auth L], B, D [auth E], F [auth G], H [auth J], J [auth L], L [auth Q]	Regulatory protein E2	DNA binding binding organic cyclic compound binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding transcription regulator activity DNA-binding transcription factor activity	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process cellular metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process cellular metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication organic cyclic compound biosynthetic process organic substance biosynthetic process viral process cellular process DNA biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process RNA metabolic process gene expression RNA biosynthetic process DNA-templated transcription	host cellular component host intracellular part host cytoskeleton host cell part host intracellular region cellular anatomical entity host intracellular organelle host intracellular membrane-bounded organelle host cell membrane host cell mitochondrion host cell cytoplasm part host cell cytoplasm host cell mitochondrial envelope host cell mitochondrial membrane host cellular component host intracellular part host cytoskeleton host cell part host intracellular region cellular anatomical entity host intracellular organelle host intracellular membrane-bounded organelle host cell membrane host cell mitochondrion host cell cytoplasm part host cell cytoplasm host cell mitochondrial envelope host cell mitochondrial membrane host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth D], E [auth F], G [auth H], I [auth K], A, C [auth D], E [auth F], G [auth H], I [auth K], K [auth M]	IPR046935	DNA helicase E1, DNA-binding domain superfamily, papillomavirus	Homologous Superfamily
A, C [auth D], E [auth F], G [auth H], I [auth K], A, C [auth D], E [auth F], G [auth H], I [auth K], K [auth M]	IPR046832	DNA helicase E1, DNA-binding domain, papillomavirus	Domain
A, C [auth D], E [auth F], G [auth H], I [auth K], A, C [auth D], E [auth F], G [auth H], I [auth K], K [auth M]	IPR001177	DNA helicase E1, C-terminal, Papillomavirus	Domain
A, C [auth D], E [auth F], G [auth H], I [auth K], A, C [auth D], E [auth F], G [auth H], I [auth K], K [auth M]	IPR014000	DNA helicase E1, N-terminal, Papillomavirus	Domain
A, C [auth D], E [auth F], G [auth H], I [auth K], A, C [auth D], E [auth F], G [auth H], I [auth K], K [auth M]	IPR037102	Zinc finger, large T-antigen D1 domain superfamily	Homologous Superfamily
A, C [auth D], E [auth F], G [auth H], I [auth K], A, C [auth D], E [auth F], G [auth H], I [auth K], K [auth M]	IPR016393	Replication protein E1, papillomavirus	Family
A, C [auth D], E [auth F], G [auth H], I [auth K], A, C [auth D], E [auth F], G [auth H], I [auth K], K [auth M]	IPR014015	Helicase, superfamily 3, DNA virus	Domain
A, C [auth D], E [auth F], G [auth H], I [auth K], A, C [auth D], E [auth F], G [auth H], I [auth K], K [auth M]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D [auth E], F [auth G], H [auth J], J [auth L], B, D [auth E], F [auth G], H [auth J], J [auth L], L [auth Q]	IPR033668	Regulatory protein E2	Family
B, D [auth E], F [auth G], H [auth J], J [auth L], B, D [auth E], F [auth G], H [auth J], J [auth L], L [auth Q]	IPR042503	E2 regulatory, transactivation domain, subdomain 1	Homologous Superfamily
B, D [auth E], F [auth G], H [auth J], J [auth L], B, D [auth E], F [auth G], H [auth J], J [auth L], L [auth Q]	IPR001866	Papillomavirus E2, N-terminal	Domain
B, D [auth E], F [auth G], H [auth J], J [auth L], B, D [auth E], F [auth G], H [auth J], J [auth L], L [auth Q]	IPR036050	E2 regulatory, transactivation domain	Homologous Superfamily
B, D [auth E], F [auth G], H [auth J], J [auth L], B, D [auth E], F [auth G], H [auth J], J [auth L], L [auth Q]	IPR042504	E2 regulatory, transactivation domain, subdomain 2	Homologous Superfamily
B, D [auth E], F [auth G], H [auth J], J [auth L], B, D [auth E], F [auth G], H [auth J], J [auth L], L [auth Q]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
B, D [auth E], F [auth G], H [auth J], J [auth L], B, D [auth E], F [auth G], H [auth J], J [auth L], L [auth Q]	IPR000427	Papillomavirus E2, C-terminal	Domain
B, D [auth E], F [auth G], H [auth J], J [auth L], B, D [auth E], F [auth G], H [auth J], J [auth L], L [auth Q]	IPR035975	E2/EBNA1, C-terminal	Homologous Superfamily

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.