3L10

Structure of split monoubiquitinated PCNA with ubiquitin in position one

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3l10a1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	automated matches	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	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)
A	PCNA_N	e3l10A1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N	ECOD (1.6)
B	ubiquitin_1	e3l10B3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	PCNA_C	e3l10B2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.150.10	Alpha Beta	Roll	DNA Polymerase III	Chain A, domain 2	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.150.10	Alpha Beta	Roll	DNA Polymerase III	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
A	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
B	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
B	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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
B	Monoubiquitinated Proliferating cell nuclear antigen	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding structural molecule activity structural constituent of ribosome cation binding ion binding metal ion binding small molecule binding DNA binding protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding structural molecule activity structural constituent of ribosome cation binding ion binding metal ion binding small molecule binding DNA 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	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process cytoplasmic translation metabolic process cellular process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing cellular component biogenesis nucleobase-containing compound metabolic process ribosome biogenesis maturation of SSU-rRNA maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) cellular component organization or biogenesis RNA processing rRNA metabolic process ribosomal small subunit biogenesis nucleic acid metabolic process organic cyclic compound metabolic process ncRNA metabolic process nucleic acid catabolic process organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis organic substance catabolic process organelle assembly protein-containing complex organization non-membrane-bounded organelle assembly ribosomal small subunit assembly protein-RNA complex assembly cellular component organization organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly ribosome assembly protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal cell cycle mitotic cell cycle DNA-templated DNA replication lagging strand elongation DNA metabolic process DNA strand elongation DNA replication DNA strand elongation involved in DNA replication 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 DNA synthesis involved in DNA repair nucleic acid biosynthetic process translesion synthesis nucleobase-containing compound biosynthetic process error-free translesion synthesis 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 chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process regulation of cellular metabolic process 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 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle PCNA complex nuclear protein-containing complex enzyme activator complex DNA polymerase processivity factor complex replication fork chromosome chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR046938	DNA clamp superfamily	Homologous Superfamily
A	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
A	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
A	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
A	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
B	IPR019954	Ubiquitin conserved site	Conserved Site
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR038582	Small ribosomal subunit protein eS31 eukaryotic-type superfamily	Homologous Superfamily
B	IPR002906	Small ribosomal subunit protein eS31	Domain
B	IPR019956	Ubiquitin domain	Domain
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily
B	IPR046938	DNA clamp superfamily	Homologous Superfamily
B	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
B	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
B	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
B	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site

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.