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
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]	PF00705	e7kc0F2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF00705	ECOD (1.6)
C [auth F]	PF02747	e7kc0F1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF02747	ECOD (1.6)
G [auth E]	PF00705	e7kc0E1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF00705	ECOD (1.6)
G [auth E]	PF02747	e7kc0E2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF02747	ECOD (1.6)
H [auth G]	PF00705	e7kc0G2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF00705	ECOD (1.6)
H [auth G]	PF02747	e7kc0G1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF02747	ECOD (1.6)
E [auth B]	PF18018	e7kc0B2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF18018	ECOD (1.6)
E [auth B]	PF04042	e7kc0B1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PF04042	ECOD (1.6)
F [auth C]	F_UNCLASSIFIED	e7kc0C1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)

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]	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
D [auth A]	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	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 organic cyclic compound 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 organic cyclic compound metabolic process DNA strand elongation organic substance metabolic process DNA replication 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 organic cyclic compound metabolic process DNA strand elongation organic substance metabolic process 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 process meiotic mismatch repair cellular response to stress response to stress cell cycle process DNA repair meiotic cell cycle meiosis I cell cycle process DNA damage response postreplication repair cellular biosynthetic process DNA synthesis involved in DNA repair nucleic acid biosynthetic process organic substance biosynthetic process translesion synthesis cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process error-free translesion synthesis biosynthetic process organic cyclic compound biosynthetic process DNA biosynthetic 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 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 regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization 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 protein-containing complex organization epigenetic regulation of gene expression negative regulation of metabolic process regulation of cellular metabolic process gene expression negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process 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 positive regulation of cellular process regulation of DNA repair regulation of response to stimulus maintenance of DNA repeat elements maintenance of DNA trinucleotide repeats subtelomeric heterochromatin formation telomere organization nucleotide-excision repair	membrane-bounded organelle protein-containing complex intracellular anatomical structure PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity enzyme activator complex DNA polymerase processivity factor complex intracellular organelle organelle intracellular non-membrane-bounded organelle replication fork membrane-bounded organelle protein-containing complex intracellular anatomical structure PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity enzyme activator complex DNA polymerase processivity factor complex intracellular organelle organelle intracellular non-membrane-bounded organelle replication fork chromosome non-membrane-bounded organelle chromosome, telomeric region chromosomal region
D [auth A]	DNA polymerase	binding nucleoside phosphate binding organic cyclic compound 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 binding nucleoside phosphate binding organic cyclic compound 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 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 replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process 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 replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process organic substance 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 cellular process DNA repair 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 nucleotide-excision repair, DNA gap filling nucleotide-excision repair base-excision repair, gap-filling base-excision repair	intracellular anatomical structure cytoplasm cellular anatomical entity 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 intracellular anatomical structure cytoplasm cellular anatomical entity 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 replication fork non-membrane-bounded organelle delta DNA polymerase complex catalytic complex protein-DNA complex nuclear replication fork intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular non-membrane-bounded 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 organic cyclic compound binding nucleic acid binding	DNA-templated DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA strand elongation organic substance metabolic process DNA replication metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process lagging strand elongation leading strand elongation DNA-templated DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA strand elongation organic substance metabolic process DNA replication metabolic 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 organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process organic substance 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 cellular process DNA repair mismatch repair nucleotide-excision repair 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 postreplication repair	intracellular anatomical structure cytoplasm cellular anatomical entity 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 intracellular anatomical structure cytoplasm cellular anatomical entity 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 replication fork non-membrane-bounded organelle delta DNA polymerase complex catalytic complex protein-DNA complex nuclear replication fork intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular non-membrane-bounded organelle intracellular protein-containing complex 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	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress metabolic process cellular process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA replication DNA strand elongation involved in DNA replication 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 DNA replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process organic substance catabolic process RNA catabolic process base-excision repair 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	membrane-bounded organelle protein-containing 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 membrane-bounded organelle protein-containing 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 delta DNA polymerase complex catalytic complex protein-DNA complex nuclear replication fork intracellular membrane-bounded organelle cellular anatomical entity DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular non-membrane-bounded organelle intracellular protein-containing complex 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]	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

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.