4Y97

Crystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	SCOP2 Family	DNA polymerase alpha OB-fold domain-like	8050855	4007079	SCOP2 (2022-06-29)
A	SCOP2 Family	DNA polymerase subunit-like	8045194	4004346	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8053380	3000135	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Metallo-dependent phosphatases	8053379	3001067	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Metallo-dependent phosphatases	8053379	3001067	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8053380	3000135	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleic acid-binding proteins	8053380	3000135	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Metallo-dependent phosphatases	8053379	3001067	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Metallo-dependent phosphatases	8053379	3001067	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Nucleic acid-binding proteins	8053380	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Zinc finger domain of DNA polymerase-alpha	8032318	3001751	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Zinc finger domain of DNA polymerase-alpha	8032318	3001751	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Zinc finger domain of DNA polymerase-alpha	8032318	3001751	SCOP2B (2022-06-29)
H	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)
A	KOG1625_2nd	e4y97A2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG1625_2nd	ECOD (1.6)
A	DNA_pol_E_B	e4y97A1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: DNA_pol_E_B	ECOD (1.6)
C	KOG1625_2nd	e4y97C1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG1625_2nd	ECOD (1.6)
C	DNA_pol_E_B	e4y97C2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: DNA_pol_E_B	ECOD (1.6)
E	KOG1625_2nd	e4y97E2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG1625_2nd	ECOD (1.6)
E	DNA_pol_E_B	e4y97E1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: DNA_pol_E_B	ECOD (1.6)
G	KOG1625_2nd	e4y97G1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG1625_2nd	ECOD (1.6)
G	DNA_pol_E_B	e4y97G2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: DNA_pol_E_B	ECOD (1.6)
B	zf-DNA_Pol_N	e4y97B2	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: zf-DNA_Pol_N	ECOD (1.6)
B	zf-DNA_Pol_C	e4y97B1	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: zf-DNA_Pol_C	ECOD (1.6)
D	zf-DNA_Pol_N	e4y97D2	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: zf-DNA_Pol_N	ECOD (1.6)
D	zf-DNA_Pol_C	e4y97D1	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: zf-DNA_Pol_C	ECOD (1.6)
F	zf-DNA_Pol_N	e4y97F2	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: zf-DNA_Pol_N	ECOD (1.6)
F	zf-DNA_Pol_C	e4y97F1	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: zf-DNA_Pol_C	ECOD (1.6)
H	zf-DNA_Pol_N	e4y97H1	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: zf-DNA_Pol_N	ECOD (1.6)
H	zf-DNA_Pol_C	e4y97H2	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: zf-DNA_Pol_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.3200.20	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af0941	DNA Polymerase alpha, zinc finger	CATH (4.3.0)
D	1.10.3200.20	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af0941	DNA Polymerase alpha, zinc finger	CATH (4.3.0)
F	1.10.3200.20	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af0941	DNA Polymerase alpha, zinc finger	CATH (4.3.0)
H	1.10.3200.20	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af0941	DNA Polymerase alpha, zinc finger	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family
A, C, E, G	PF08418	DNA polymerase alpha subunit B N-terminal (Pol_alpha_B_N)	DNA polymerase alpha subunit B N-terminal	This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation [1]. This domain adopts an OB fold [2].	Domain
B, D, F, H	PF08996	DNA Polymerase alpha zinc finger (zf-DNA_Pol)	DNA Polymerase alpha zinc finger	The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parall ...	The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	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
B, D, F, H	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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

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

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.