8QJ7

Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2B Superfamily	Zinc finger domain of DNA polymerase-alpha	8032318	3001751	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Metallo-dependent phosphatases	8053379	3001067	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Nucleic acid-binding proteins	8053380	3000135	SCOP2B (2022-06-29)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	DNA primase small subunit	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding DNA-directed 5'-3' RNA polymerase activity DNA primase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding DNA-directed 5'-3' RNA polymerase activity DNA primase 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 transition metal ion binding zinc ion binding	DNA-templated DNA replication DNA replication initiation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process cellular biosynthetic process DNA replication, synthesis of primer cellular metabolic process DNA-templated DNA replication DNA replication initiation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process cellular biosynthetic process DNA replication, synthesis of primer cellular metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process cellular 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 nuclear replisome replication fork 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 nuclear replisome replication fork non-membrane-bounded organelle catalytic complex protein-DNA complex nuclear replication fork intracellular membrane-bounded organelle cellular anatomical entity DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex intracellular non-membrane-bounded organelle DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome membrane nucleoplasm
B [auth A]	DNA polymerase alpha catalytic subunit	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 nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding protein-containing complex binding chromatin 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 nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding protein-containing complex binding chromatin 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 protein binding kinase binding enzyme binding protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding single-stranded DNA binding	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 DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA strand elongation involved in DNA replication DNA replication initiation 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 DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA strand elongation involved in DNA replication DNA replication initiation leading strand elongation multicellular organismal process regulation of cellular process cellular biosynthetic process cytokine production organic substance biosynthetic process regulation of cytokine production regulation of multicellular organismal process regulation of biosynthetic process regulation of biological process type I interferon production cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process cellular process regulation of macromolecule biosynthetic process regulation of metabolic process regulation of type I interferon production DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process organic cyclic compound biosynthetic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair mitotic DNA replication cell cycle DNA replication initiation nuclear DNA replication cell cycle DNA replication mitotic DNA replication initiation mitotic cell cycle nuclear cell cycle DNA replication initiation mitotic cell cycle process cell cycle cell cycle process DNA synthesis involved in DNA repair DNA biosynthetic process double-strand break repair double-strand break repair via nonhomologous end joining	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix nucleolus membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix nucleolus intracellular non-membrane-bounded organelle non-membrane-bounded organelle organelle envelope nuclear envelope endomembrane system cytoplasm cytosol nucleoplasm protein-containing complex protein-DNA complex chromatin chromosome alpha DNA polymerase:primase complex nuclear protein-containing complex nuclear chromosome transferase complex nuclear replisome replication fork catalytic complex nuclear replication fork DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex replisome
C [auth B]	DNA polymerase alpha subunit B	DNA binding binding organic cyclic compound binding nucleic acid binding	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 DNA-templated DNA replication DNA replication initiation protein localization establishment of protein localization cellular localization 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 DNA-templated DNA replication DNA replication initiation protein localization establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport organic substance transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport cellular macromolecule localization macromolecule localization protein localization to organelle establishment of localization in cell protein import into nucleus cellular process intracellular protein transport cellular biosynthetic process DNA replication, synthesis of primer cellular metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle nuclear replisome replication fork non-membrane-bounded organelle catalytic complex protein-DNA complex nuclear replication fork 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 intracellular non-membrane-bounded organelle DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome nucleoplasm
D	DNA primase large subunit	DNA binding binding organic cyclic compound 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 DNA/RNA hybrid binding	DNA-templated DNA replication DNA replication initiation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process regulation of cellular process regulation of catalytic activity regulation of transferase activity DNA-templated DNA replication DNA replication initiation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process regulation of cellular process regulation of catalytic activity regulation of transferase activity positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of molecular function biosynthetic process positive regulation of DNA metabolic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process regulation of DNA metabolic process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of molecular function positive regulation of biosynthetic process regulation of DNA primase activity positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of transferase activity biological regulation positive regulation of catalytic activity regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process cellular process positive regulation of DNA primase activity positive regulation of cellular biosynthetic process DNA replication, synthesis of primer	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 nuclear replisome replication fork 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 nuclear replisome replication fork non-membrane-bounded organelle catalytic complex protein-DNA complex nuclear replication fork intracellular membrane-bounded organelle cellular anatomical entity DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex intracellular non-membrane-bounded organelle DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C]	IPR002755	DNA primase, small subunit	Family
A [auth C]	IPR014052	DNA primase, small subunit, eukaryotic/archaeal	Family
B [auth A]	IPR038256	DNA polymerase alpha, zinc finger domain superfamily	Homologous Superfamily
B [auth A]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B [auth A]	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
B [auth A]	IPR045846	DNA polymerase alpha catalytic subunit, catalytic domain	Domain
B [auth A]	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
B [auth A]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B [auth A]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
B [auth A]	IPR015088	Zinc finger, DNA-directed DNA polymerase, family B, alpha	Domain
B [auth A]	IPR006172	DNA-directed DNA polymerase, family B	Family
B [auth A]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B [auth A]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
B [auth A]	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
B [auth A]	IPR024647	DNA polymerase alpha catalytic subunit, N-terminal domain	Domain
C [auth B]	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
C [auth B]	IPR043034	DNA polymerase alpha, subunit B, N-terminal domain superfamily	Homologous Superfamily
C [auth B]	IPR013627	DNA polymerase alpha, subunit B, N-terminal	Domain
C [auth B]	IPR016722	DNA polymerase alpha, subunit B	Family
D	IPR016558	DNA primase, large subunit, eukaryotic	Family
D	IPR007238	DNA primase large subunit, eukaryotic/archaeal	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C]	Pharos: P49642	adrenal cortex carcinoma large cell medulloblastoma malignant colon neoplasm medulloblastoma Sjogren syndrome atrial fibrillation lung cancer malignant glioma non-small cell lung carcinoma glioblastoma lymphoplasmacytic lymphoma malignant mesothelioma primitive neuroectodermal tumor
B [auth A]	Pharos: P09884	X-linked reticulate pigmentary disorder ovarian cancer PIGMENTARY DISORDER, RETICULATE, WITH SYSTEMIC MANIFESTATIONS acute lymphoblastic leukemia atypical teratoid rhabdoid tumor intellectual disability malignant mesothelioma neurofibromatosis type 1 pancreatic adenocarcinoma primitive neuroectodermal tumor acute myeloid leukemia B-cell chronic lymphocytic leukemia large cell medulloblastoma malignant colon neoplasm mantle cell lymphoma X-linked reticulate pigmentary disorder ovarian cancer PIGMENTARY DISORDER, RETICULATE, WITH SYSTEMIC MANIFESTATIONS acute lymphoblastic leukemia atypical teratoid rhabdoid tumor intellectual disability malignant mesothelioma neurofibromatosis type 1 pancreatic adenocarcinoma primitive neuroectodermal tumor acute myeloid leukemia B-cell chronic lymphocytic leukemia large cell medulloblastoma malignant colon neoplasm mantle cell lymphoma non-small cell lung carcinoma tuberculosis acute promyelocytic leukemia glioblastoma malignant glioma medulloblastoma N syndrome
C [auth B]	Pharos: Q14181	large cell medulloblastoma osteosarcoma malignant mesothelioma non-small cell lung carcinoma
D	Pharos: P49643	atypical teratoid rhabdoid tumor heart disease lung cancer medulloblastoma primitive neuroectodermal tumor Gaucher disease large cell medulloblastoma malignant ependymoma non-small cell lung carcinoma psoriasis glioblastoma lung adenocarcinoma malignant glioma osteosarcoma

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 R01GM133198.

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8QJ7

Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation