8FOJ | pdb_00008foj

Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the post RNA handoff state

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
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)
D [auth C]	SCOP2B Superfamily	Nucleic acid-binding proteins	8053388	3000135	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Metallo-dependent phosphatases	8053387	3001067	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth 1]	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
A [auth 1]	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
B [auth A]	PF01896	DNA primase small subunit (DNA_primase_S)	DNA primase small subunit	-	Family
C [auth B]	PF04104	Eukaryotic and archaeal DNA primase, large subunit C-terminal domain (DNA_primase_lrg)	Eukaryotic and archaeal DNA primase, large subunit C-terminal domain	DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 ( ...	DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae) [1]. The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase [4]. This entry represents the C-terminal alpha helical domain.	Domain
D [auth C]	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family
D [auth C]	PF22062	DNA polymerase alpha subunit B, OB domain (OB_DPOA2)	DNA polymerase alpha subunit B, OB domain	This entry represents the OB domain of DNA polymerase alpha subunit B [1-4]. B subunits of DNA polymerases stabilize the catalytic subunit, play a role in regulation of the DNA synthesis in a cell cycle-dependent manner and act as scaffolds mediating ...	This entry represents the OB domain of DNA polymerase alpha subunit B [1-4]. B subunits of DNA polymerases stabilize the catalytic subunit, play a role in regulation of the DNA synthesis in a cell cycle-dependent manner and act as scaffolds mediating interactions with other components of the replication machinery [1-4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 1]	DNA polymerase	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups H3-H4 histone complex chaperone activity protein carrier chaperone histone chaperone activity molecular carrier activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding single-stranded DNA binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA strand elongation involved in DNA replication DNA replication initiation sexual reproduction nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA strand elongation involved in DNA replication DNA replication initiation sexual reproduction reproductive process meiotic cell cycle nuclear DNA replication cell cycle DNA replication meiotic cell cycle process premeiotic DNA replication cell cycle cell cycle process leading strand elongation nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process mitotic DNA replication cell cycle DNA replication initiation mitotic DNA replication initiation mitotic cell cycle nuclear cell cycle DNA replication initiation mitotic cell cycle process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair DNA synthesis involved in DNA repair	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membraneless organelle replication fork intracellular membraneless organelle chromosome protein-containing complex alpha DNA polymerase:primase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membraneless organelle replication fork intracellular membraneless organelle chromosome protein-containing complex alpha DNA polymerase:primase complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome transferase complex intracellular organelle lumen nuclear replisome nucleoplasm catalytic complex protein-DNA complex nuclear replication fork DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome
B [auth A]	DNA primase	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 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 DNA-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 cation binding metal ion binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication DNA replication initiation DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication DNA replication initiation DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process	membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome nucleoplasm membraneless organelle replication fork catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome
C [auth B]	DNA primase large subunit	DNA binding binding nucleic acid binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication DNA replication initiation cellular response to stimulus double-strand break repair response to stimulus cellular response to stress nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication DNA replication initiation cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process	membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome nucleoplasm membraneless organelle replication fork catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome organelle envelope nuclear envelope endomembrane system
D [auth C]	DNA polymerase alpha subunit B	DNA binding binding nucleic acid binding	primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA replication primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA replication DNA replication initiation telomere organization chromosome organization telomere maintenance cellular component organization organelle organization telomere capping cellular component organization or biogenesis	membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome nucleoplasm membraneless organelle replication fork catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome organelle envelope nuclear envelope endomembrane system
E [auth T]	template DNA	-	-	-
F [auth P]	Primer RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 1]	IPR038256	DNA polymerase alpha, zinc finger domain superfamily	Homologous Superfamily
A [auth 1]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A [auth 1]	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A [auth 1]	IPR045846	DNA polymerase alpha catalytic subunit, catalytic domain	Domain
A [auth 1]	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A [auth 1]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A [auth 1]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
A [auth 1]	IPR015088	Zinc finger, DNA-directed DNA polymerase, family B, alpha	Domain
A [auth 1]	IPR006172	DNA-directed DNA polymerase, family B	Family
A [auth 1]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A [auth 1]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A [auth 1]	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A [auth 1]	IPR024647	DNA polymerase alpha catalytic subunit, N-terminal domain	Domain
B [auth A]	IPR002755	DNA primase, small subunit	Family
B [auth A]	IPR014052	DNA primase, small subunit, eukaryotic/archaeal	Family
C [auth B]	IPR016558	DNA primase, large subunit, eukaryotic	Family
C [auth B]	IPR007238	DNA primase large subunit, eukaryotic/archaeal	Family
D [auth C]	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
D [auth C]	IPR054300	DNA polymerase alpha subunit B, OB domain	Domain
D [auth C]	IPR016722	DNA polymerase alpha, subunit B	Family