7KC0

Structure of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp

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)
C [auth F]	SCOP2B Superfamily	DNA clamp	8036432	3000780	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	DNA clamp	8036430	3000780	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	DNA clamp	8036432	3000780	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	DNA clamp	8036430	3000780	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	DNA clamp	8036432	3000780	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	DNA clamp	8036430	3000780	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)
C [auth F]	PCNA_N	e7kc0F2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N	ECOD (1.6)
C [auth F]	PCNA_C	e7kc0F1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
G [auth E]	PCNA_N	e7kc0E1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N	ECOD (1.6)
G [auth E]	PCNA_C	e7kc0E2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
H [auth G]	PCNA_N	e7kc0G2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N	ECOD (1.6)
H [auth G]	PCNA_C	e7kc0G1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
E [auth B]	KOG2732	e7kc0B2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG2732	ECOD (1.6)
E [auth B]	DNA_pol_E_B	e7kc0B1	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)
F [auth C]	F_UNCLASSIFIED	e7kc0C1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth B]	3.60.21.50	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (utative)
E [auth B]	2.40.50.430	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth F], G [auth E], H [auth G]	PF02747	Proliferating cell nuclear antigen, C-terminal domain (PCNA_C)	Proliferating cell nuclear antigen, C-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
C [auth F], G [auth E], H [auth G]	PF00705	Proliferating cell nuclear antigen, N-terminal domain (PCNA_N)	Proliferating cell nuclear antigen, N-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
D [auth A]	PF14260	C4-type zinc-finger of DNA polymerase delta (zf-C4pol)	C4-type zinc-finger of DNA polymerase delta	In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1 [1]. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and thr ...	In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1 [1]. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1 [2].	Domain
D [auth A]	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
D [auth A]	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
E [auth B]	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family
E [auth B]	PF18018	DNA polymerase delta subunit OB-fold domain (DNA_pol_D_N)	DNA polymerase delta subunit OB-fold domain	The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance [1]. Human Pol delta consists of four subunits: p125, p50, p66 and p12. The first three subunits correspond ...	The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance [1]. Human Pol delta consists of four subunits: p125, p50, p66 and p12. The first three subunits correspond to the three subunits of S. cerevisiae Pol delta. p50 serves as a scaffold for the assembly of Pol delta by interacting simultaneously with all of the other three subunits. This entry corresponds to the OB fold domain found in the p50 subunit.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth P]	DNA (5'-D(PAPTPGPAPCPCPAPTPGPAPTPTPAPCPGPAPAPTPTPGP*C)-3')	-	-	-
B [auth T]	DNA (25-MER)	-	-	-
C [auth F], G [auth E], H [auth G]	Proliferating cell nuclear antigen	DNA binding binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein binding	cellular process cell cycle mitotic cell cycle DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process cellular process cell cycle mitotic cell cycle DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process leading strand elongation cellular response to stimulus mismatch repair sexual reproduction response to stimulus reproductive process meiotic cell cycle meiotic cell cycle process meiotic mismatch repair meiosis I cell cycle process cellular response to stress DNA damage response response to stress cell cycle process DNA repair translesion synthesis postreplication repair nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process error-free translesion synthesis nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process gene expression regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process mitotic sister chromatid cohesion establishment of mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion organelle organization mitotic cell cycle process establishment of sister chromatid cohesion regulation of cellular response to stress positive regulation of response to stimulus positive regulation of DNA repair regulation of response to stress regulation of DNA repair regulation of response to stimulus maintenance of DNA repeat elements maintenance of DNA trinucleotide repeats subtelomeric heterochromatin formation nucleotide-excision repair	membrane-bounded organelle protein-containing complex intracellular anatomical structure PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle enzyme activator complex DNA polymerase processivity factor complex intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork membrane-bounded organelle protein-containing complex intracellular anatomical structure PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle enzyme activator complex DNA polymerase processivity factor complex intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
D [auth A]	DNA polymerase	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity catalytic activity DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding nucleic acid binding molecular adaptor activity 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 replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic 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 replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity cellular response to stimulus response to stimulus DNA replication proofreading cellular response to stress DNA damage response response to stress DNA repair nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process nucleotide-excision repair, DNA gap filling nucleotide-excision repair base-excision repair, gap-filling base-excision repair double-strand break repair double-strand break repair via nonhomologous end joining	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle nuclear replisome membraneless organelle replication fork delta DNA polymerase complex catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular protein-containing complex nuclear lumen replisome
E [auth B]	POL31 isoform 1	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 DNA binding binding nucleic acid binding	DNA-templated DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process lagging strand elongation leading strand elongation DNA replication, removal of RNA primer DNA-templated DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process lagging strand elongation leading strand elongation DNA replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process cellular response to stimulus response to stimulus base-excision repair cellular response to stress DNA damage response response to stress DNA repair mismatch repair nucleotide-excision repair nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process postreplication repair	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle nuclear replisome membraneless organelle replication fork delta DNA polymerase complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle organelle lumen organelle nuclear lumen replisome
F [auth C]	POL32 isoform 1	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	DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process leading strand elongation translesion synthesis DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process leading strand elongation translesion synthesis cellular response to stimulus postreplication repair response to stimulus nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid biosynthetic process cellular response to stress biosynthetic process DNA damage response response to stress error-prone translesion synthesis DNA biosynthetic process DNA repair DNA replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process base-excision repair nucleotide-excision repair RNA-templated DNA biosynthetic process DNA amplification double-strand break repair DNA recombination double-strand break repair via break-induced replication recombinational repair double-strand break repair via homologous recombination	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork delta DNA polymerase complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle organelle lumen organelle nuclear lumen replisome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth F], G [auth E], H [auth G]	IPR046938	DNA clamp superfamily	Homologous Superfamily
C [auth F], G [auth E], H [auth G]	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
C [auth F], G [auth E], H [auth G]	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
C [auth F], G [auth E], H [auth G]	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
C [auth F], G [auth E], H [auth G]	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
D [auth A]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
D [auth A]	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
D [auth A]	IPR050240	DNA polymerase type-B	Family
D [auth A]	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
D [auth A]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
D [auth A]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
D [auth A]	IPR006172	DNA-directed DNA polymerase, family B	Family
D [auth A]	IPR025687	C4-type zinc-finger of DNA polymerase delta	Domain
D [auth A]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
D [auth A]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
D [auth A]	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
E [auth B]	IPR024826	DNA polymerase delta/II small subunit family	Family
E [auth B]	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
E [auth B]	IPR040663	DNA polymerase delta subunit, OB-fold domain	Domain
E [auth B]	IPR041863	DNA polymerase delta subunit 2, C-terminal domain	Domain