1KSY

Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex

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)
D [auth A]	d1ksya_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication initiation protein E1	Replication initiation protein E1	(Bovine papillomavirus ) [TaxId: 10571 ],	SCOPe (2.08)
E [auth B]	d1ksyb1	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication initiation protein E1	Replication initiation protein E1	(Bovine papillomavirus ) [TaxId: 10571 ],	SCOPe (2.08)
E [auth B]	d1ksyb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bovine papillomavirus ) [TaxId: 10571 ],	SCOPe (2.08)
F [auth C]	d1ksyc_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication initiation protein E1	Replication initiation protein E1	(Bovine papillomavirus ) [TaxId: 10571 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth A]	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8032862	3001937	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8032862	3001937	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8032862	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)
D [auth A]	PF20450	e1ksyA1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF20450	ECOD (1.6)
E [auth B]	PF20450	e1ksyB1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF20450	ECOD (1.6)
F [auth C]	PF20450	e1ksyC1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF20450	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth A]	3.40.1310.10	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
E [auth B]	3.40.1310.10	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
F [auth C]	3.40.1310.10	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A], E [auth B], F [auth C]	PF20450	Papillomavirus E1, DNA-binding domain (PPV_E1_DBD)	Papillomavirus E1, DNA-binding domain	This is the DNA-binding domain (DBD) 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 at the origin of replication (ori) [1,2]. This d ...	This is the DNA-binding domain (DBD) 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 at the origin of replication (ori) [1,2]. This domain is found in the central region of E1 and binds DNA at specific sites of viral origin, and also binds cooperatively with E2-DBD. This domain comprises a five-stranded antiparallel beta-sheet flanked by alpha helices on each side [2]. This domain binds originally as a dimer in which each monomer binds to one half-site of the palindromic E1 binding site, and promotes the assembly of the hexameric helicase on the ori [2]. E1 has a domain architecture and function similar to SV40 T-antigen [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], B [auth E]	E1 Recognition Sequence, Strand 1	-	-	-
C [auth F]	E1 Recognition Sequence, Strand 2	-	-	-
D [auth A], E [auth B], F [auth C]	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	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A], E [auth B], F [auth C]	IPR046935	DNA helicase E1, DNA-binding domain superfamily, papillomavirus	Homologous Superfamily
D [auth A], E [auth B], F [auth C]	IPR046832	DNA helicase E1, DNA-binding domain, papillomavirus	Domain
D [auth A], E [auth B], F [auth C]	IPR001177	DNA helicase E1, C-terminal, Papillomavirus	Domain
D [auth A], E [auth B], F [auth C]	IPR014000	DNA helicase E1, N-terminal, Papillomavirus	Domain
D [auth A], E [auth B], F [auth C]	IPR037102	Zinc finger, large T-antigen D1 domain superfamily	Homologous Superfamily
D [auth A], E [auth B], F [auth C]	IPR016393	Replication protein E1, papillomavirus	Family
D [auth A], E [auth B], F [auth C]	IPR014015	Helicase, superfamily 3, DNA virus	Domain
D [auth A], E [auth B], F [auth C]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.