8D9D | pdb_00008d9d

Human DNA polymerase-alpha/primase elongation complex II bound to primer/template

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
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)
D	SCOP2B Superfamily	Metallo-dependent phosphatases	8053379	3001067	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleic acid-binding proteins	8053380	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Zinc finger domain of DNA polymerase-alpha	8032318	3001751	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	F_UNCLASSIFIED	e8d9dD2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e8d9dD1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8d9dC6	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8d9dC5	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8d9dC7	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8d9dC1	A: a+b two layers	X: Alpha-beta plaits	H: Family B DNA polymerase insertion domain (From Topology)	T: Family B DNA polymerase insertion domain	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8d9dC4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8d9dC2	A: few secondary structure elements	X: Rubredoxin-like	H: Zinc finger domain of DNA polymerase-alpha (From Topology)	T: Zinc finger domain of DNA polymerase-alpha	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8d9dB2	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Fe-S cluster domain of DNA primase	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8d9dB1	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: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8d9dA1	A: alpha arrays	X: Insert all-alpha domain in prim-pol (From Topology)	H: Insert all-alpha domain in prim-pol (From Topology)	T: Insert all-alpha domain in prim-pol	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8d9dA2	A: a+b complex topology	X: Prim-pol domain (From Topology)	H: Prim-pol domain (From Topology)	T: Prim-pol domain	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family
D	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
C	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
C	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
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
A	PF01896	DNA primase small subunit (DNA_primase_S)	DNA primase small subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F	DNA (5'-D(APTPGPGPTPCPGPTPGPCPCPGPCPCPAPAPTPAP*A)-3')	-	-	-
E	DNA/RNA (5'-D((GTP))-R(PGPCPGPGPCPAPCPG)-D(PAPCPC)-3')	-	-	-
D	DNA polymerase alpha subunit B	DNA binding binding nucleic acid 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 establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport 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 establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular 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 nuclear replisome nucleoplasm membraneless organelle replication fork catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle 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 cilium plasma membrane bounded cell projection ciliary basal body cell projection microtubule organizing center cytoskeleton microtubule cytoskeleton
C	DNA polymerase alpha catalytic subunit	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 catalytic activity, acting on DNA DNA-directed DNA polymerase activity 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 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 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 leading strand elongation 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 leading strand elongation regulation of biosynthetic process multicellular organismal process regulation of biological process regulation of cellular process type I interferon production biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process cytokine production regulation of cytokine production regulation of macromolecule biosynthetic process regulation of multicellular organismal 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 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 intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membraneless organelle organelle envelope nuclear envelope endomembrane system cytoplasm cytosol nucleoplasm chromatin chromosome protein-containing complex alpha DNA polymerase:primase complex nuclear protein-containing complex nuclear chromosome transferase complex nuclear replisome replication fork catalytic complex protein-DNA 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
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 DNA/RNA hybrid binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process 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
A	DNA primase small subunit	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding transition metal ion binding zinc ion binding DNA-directed RNA polymerase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding transition metal ion binding zinc ion 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	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process 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 membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR043034	DNA polymerase alpha, subunit B, N-terminal domain superfamily	Homologous Superfamily
D	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
D	IPR054300	DNA polymerase alpha subunit B, OB domain	Domain
D	IPR013627	DNA polymerase alpha, subunit B, N-terminal	Domain
D	IPR016722	DNA polymerase alpha, subunit B	Family
C	IPR038256	DNA polymerase alpha, zinc finger domain superfamily	Homologous Superfamily
C	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
C	IPR045846	DNA polymerase alpha catalytic subunit, catalytic domain	Domain
C	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
C	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
C	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
C	IPR015088	Zinc finger, DNA-directed DNA polymerase, family B, alpha	Domain
C	IPR006172	DNA-directed DNA polymerase, family B	Family
C	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
C	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
C	IPR024647	DNA polymerase alpha catalytic subunit, N-terminal domain	Domain
B	IPR016558	DNA primase, large subunit, eukaryotic	Family
B	IPR007238	DNA primase large subunit, eukaryotic/archaeal	Family
A	IPR002755	DNA primase, small subunit	Family
A	IPR014052	DNA primase, small subunit, eukaryotic/archaeal	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	Pharos: Q14181	large cell medulloblastoma osteosarcoma malignant mesothelioma non-small cell lung carcinoma
C	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
B	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
A	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