3FLO

Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B 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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metallo-dependent phosphatases	8053387	3001067	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8053388	3000135	SCOP2B (2022-06-29)
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)
G [auth E]	SCOP2 Family	DNA polymerase alpha OB-fold domain-like	8050856	4007079	SCOP2 (2022-06-29)
G [auth E]	SCOP2 Family	DNA polymerase subunit-like	8045196	4004346	SCOP2 (2022-06-29)
G [auth E]	SCOP2 Superfamily	Nucleic acid-binding proteins	8053388	3000135	SCOP2 (2022-06-29)
G [auth E]	SCOP2 Superfamily	Metallo-dependent phosphatases	8053387	3001067	SCOP2 (2022-06-29)
J [auth G]	SCOP2B Superfamily	Nucleic acid-binding proteins	8053388	3000135	SCOP2B (2022-06-29)
J [auth G]	SCOP2B Superfamily	Metallo-dependent phosphatases	8053387	3001067	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	e3floA3	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	e3floA2	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)
D [auth C]	KOG1625_2nd	e3floC1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG1625_2nd	ECOD (1.6)
D [auth C]	DNA_pol_E_B	e3floC2	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 [auth E]	KOG1625_2nd	e3floE1	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 [auth E]	DNA_pol_E_B	e3floE2	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)
J [auth G]	KOG1625_2nd	e3floG3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG1625_2nd	ECOD (1.6)
J [auth G]	DNA_pol_E_B	e3floG2	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 [auth B]	zf-DNA_Pol_N	e3floB1	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)
C [auth B]	zf-DNA_Pol_C	e3floB2	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 [auth D]	zf-DNA_Pol_N	e3floD1	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 [auth D]	zf-DNA_Pol_C	e3floD2	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)
I [auth F]	zf-DNA_Pol_N	e3floF1	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)
I [auth F]	zf-DNA_Pol_C	e3floF2	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)
L [auth H]	zf-DNA_Pol_N	e3floH1	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)
L [auth H]	zf-DNA_Pol_C	e3floH2	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)
A	3.60.21.60	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
D [auth C]	3.60.21.60	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
G [auth E]	3.60.21.60	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
J [auth G]	3.60.21.60	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
C [auth B]	1.10.3200.20	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af0941	DNA Polymerase alpha, zinc finger	CATH (4.3.0)
F [auth D]	1.10.3200.20	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af0941	DNA Polymerase alpha, zinc finger	CATH (4.3.0)
I [auth F]	1.10.3200.20	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af0941	DNA Polymerase alpha, zinc finger	CATH (4.3.0)
L [auth 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, D [auth C], G [auth E], J [auth G]	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family
A, D [auth C], G [auth E], J [auth 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
C [auth B], F [auth D], I [auth F], L [auth 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, D [auth C], G [auth E], J [auth G]	DNA polymerase alpha subunit B	DNA binding binding organic cyclic compound binding nucleic acid binding	cellular biosynthetic process cellular metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process cellular biosynthetic process cellular metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA replication initiation DNA replication 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 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 organelle envelope nuclear envelope endomembrane system
B [auth I], E [auth J], H [auth K], K [auth L]	DNA polymerase alpha catalytic subunit A	-	-	-
C [auth B], F [auth D], I [auth F], L [auth H]	DNA polymerase alpha catalytic subunit A	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 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 cation 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 sexual reproduction reproductive process meiotic cell cycle nuclear DNA replication cell cycle DNA replication meiotic cell cycle process premeiotic DNA replication cellular process cell cycle cell cycle process leading strand elongation cellular biosynthetic process cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process nucleic acid biosynthetic process biosynthetic process organic cyclic compound biosynthetic process organic substance 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 intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle intracellular non-membrane-bounded organelle replication fork chromosome non-membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle intracellular non-membrane-bounded organelle replication fork chromosome non-membrane-bounded organelle 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 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

InterPro: Protein Family Classification InterPro Database Homepage

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

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.