6S2F

Cryo-EM structure of Ctf18-1-8 in complex with the catalytic domain of DNA polymerase epsilon (Class 2)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	F_UNCLASSIFIED	e6s2fA4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF22634	e6s2fA3	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: PF22634	ECOD (1.6)
A	PF00136	e6s2fA1	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: PF00136	ECOD (1.6)
A	F_UNCLASSIFIED	e6s2fA5	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)
A	PF03104	e6s2fA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF03104	ECOD (1.6)
B [auth D]	PF09696	e6s2fD1	A: beta complex topology	X: triple barrel (From Homology)	H: triple barrel	T: Rap30/74 interaction domains-like	F: PF09696	ECOD (1.6)
D [auth B]	PF09724	e6s2fB5	A: beta complex topology	X: triple barrel (From Homology)	H: triple barrel	T: Rap30/74 interaction domains-like	F: PF09724	ECOD (1.6)
D [auth B]	PF09724	e6s2fB3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF09724	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
B [auth D]	PF09696	Ctf8 (Ctf8)	Ctf8	-	Family
D [auth B]	PF09724	Sister chromatid cohesion protein Dcc1 (Dcc1)	Sister chromatid cohesion protein Dcc1	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA polymerase epsilon catalytic subunit A	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule 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 single-stranded DNA exodeoxyribonuclease activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule 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 single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity catalytic activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding nucleic acid binding RNA binding mRNA binding double-stranded DNA binding SUMO binding protein binding ubiquitin-like protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding single-stranded DNA binding	cellular process cell cycle mitotic cell cycle cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction negative regulation of mitotic cell cycle cellular process cell cycle mitotic cell cycle cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction DNA replication checkpoint signaling regulation of cell cycle cell cycle process cell cycle G2/M phase transition regulation of biological process mitotic DNA replication checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition DNA-templated DNA replication primary metabolic process DNA metabolic process leading strand elongation 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 DNA-templated DNA replication maintenance of fidelity DNA replication proofreading cellular response to stress DNA damage response response to stress DNA repair 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 biosynthetic process organic cyclic compound biosynthetic process error-prone translesion synthesis DNA biosynthetic process base-excision repair cellular component organization organelle organization mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion cellular component organization or biogenesis nucleotide-excision repair, DNA gap filling nucleotide-excision repair base-excision repair, gap-filling double-strand break repair homologous recombination DNA recombination gene conversion DNA damage checkpoint signaling mitotic DNA damage checkpoint signaling mitotic intra-S DNA damage checkpoint signaling signal transduction in response to DNA damage double-strand break repair via nonhomologous end joining	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 non-membrane-bounded organelle catalytic complex intracellular 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 non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity epsilon DNA polymerase complex DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular non-membrane-bounded organelle intracellular protein-containing complex nuclear lumen replication fork nuclear replication fork
B [auth D]	Chromosome transmission fidelity protein 8	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 chromosome organization maintenance of DNA repeat elements cellular component organization organelle organization cellular 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 chromosome organization maintenance of DNA repeat elements cellular component organization organelle organization cellular process cellular component organization or biogenesis maintenance of DNA trinucleotide repeats mitotic sister chromatid cohesion sister chromatid cohesion cell cycle cell cycle process	membrane-bounded organelle protein-containing complex Ctf18 RFC-like complex intracellular anatomical structure nucleus nuclear protein-containing complex chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle
C [auth E]	Chromosome transmission fidelity protein 18	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity	DNA-templated DNA replication DNA replication initiation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process chromosome organization maintenance of DNA repeat elements cellular component organization DNA-templated DNA replication DNA replication initiation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process chromosome organization maintenance of DNA repeat elements cellular component organization organelle organization cellular process cellular component organization or biogenesis maintenance of DNA trinucleotide repeats cellular response to stimulus double-strand break repair response to stimulus DNA recombination cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair mitotic sister chromatid cohesion sister chromatid cohesion cell cycle cell cycle process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex Ctf18 RFC-like complex nucleus nuclear protein-containing complex chromosome intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex Ctf18 RFC-like complex nucleus nuclear protein-containing complex chromosome intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-enclosed lumen nuclear replication fork nuclear chromosome intracellular organelle lumen organelle lumen replication fork nuclear lumen
D [auth B]	Sister chromatid cohesion protein DCC1	-	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 chromosome organization maintenance of DNA repeat elements cellular component organization organelle organization cellular 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 chromosome organization maintenance of DNA repeat elements cellular component organization organelle organization cellular process cellular component organization or biogenesis maintenance of DNA trinucleotide repeats mitotic sister chromatid cohesion sister chromatid cohesion maintenance of sister chromatid cohesion maintenance of mitotic sister chromatid cohesion cell cycle cell cycle process	membrane-bounded organelle protein-containing complex Ctf18 RFC-like complex intracellular anatomical structure nucleus nuclear protein-containing complex chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle chromosome, centromeric region membrane-bounded organelle protein-containing complex Ctf18 RFC-like complex intracellular anatomical structure nucleus nuclear protein-containing complex chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle chromosome, centromeric region chromosomal region protein-DNA complex chromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
A	IPR006172	DNA-directed DNA polymerase, family B	Family
A	IPR029703	DNA polymerase epsilon catalytic subunit	Family
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR013697	DNA polymerase epsilon, catalytic subunit A, C-terminal	Domain
A	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
B [auth D]	IPR018607	Chromosome transmission fidelity protein 8	Family
C [auth E]	IPR047854	Replication factor C, lid domain	Domain
C [auth E]	IPR003593	AAA+ ATPase domain	Domain
C [auth E]	IPR003959	ATPase, AAA-type, core	Domain
C [auth E]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D [auth B]	IPR019128	Sister chromatid cohesion protein Dcc1	Family

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.