3TBL

Structure of Mono-ubiquitinated PCNA: Implications for DNA Polymerase Switching and Okazaki Fragment Maturation

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3tblb1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	Proliferating cell nuclear antigen (PCNA)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3tblc1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	Proliferating cell nuclear antigen (PCNA)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3tbla1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	Proliferating cell nuclear antigen (PCNA)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3tble_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3tbld_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8032796	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)
B	PF00705	e3tblB1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF00705	ECOD (1.6)
B	PF02747	e3tblB2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF02747	ECOD (1.6)
C	PF00705	e3tblC1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF00705	ECOD (1.6)
C	PF02747	e3tblC2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF02747	ECOD (1.6)
A	PF00705	e3tblA1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF00705	ECOD (1.6)
A	PF02747	e3tblA2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF02747	ECOD (1.6)
E	PF00240	e3tblE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
D	PF00240	e3tblD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
C	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
A	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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, B, C	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, E	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, B, C	Proliferating cell nuclear antigen	protein-containing complex binding binding hydrolase activity, acting on glycosyl bonds catalytic activity, acting on DNA purine-specific mismatch base pair DNA N-glycosylase activity catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity mismatch base pair DNA N-glycosylase activity protein tyrosine kinase binding protein binding kinase binding protein-containing complex binding binding hydrolase activity, acting on glycosyl bonds catalytic activity, acting on DNA purine-specific mismatch base pair DNA N-glycosylase activity catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity mismatch base pair DNA N-glycosylase activity protein tyrosine kinase binding protein binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding identical protein binding chromatin binding DNA binding DNA insertion or deletion binding double-stranded DNA binding organic cyclic compound binding mismatched DNA binding dinucleotide insertion or deletion binding nucleic acid binding mismatch repair complex binding MutLalpha complex binding damaged DNA binding histone acetyltransferase binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear estrogen receptor binding DNA polymerase binding	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity 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 replication fork processing leading strand elongation DNA strand elongation DNA strand elongation involved in DNA replication ovulation cycle rhythmic process estrous cycle reproductive process multicellular organismal reproductive process cellular response to stimulus mismatch repair response to stimulus cellular response to stress DNA damage response response to stress cellular process DNA repair 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 epithelium development cellular developmental process cell differentiation tissue development epithelial cell differentiation 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 DNA biosynthetic process regulation of cellular process 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 response to organic substance response to ketone response to lipid response to endogenous stimulus response to glucocorticoid response to oxygen-containing compound response to corticosteroid response to hormone response to steroid hormone response to chemical response to dexamethasone response to organic cyclic compound response to acid chemical response to organonitrogen compound response to nitrogen compound response to L-glutamate response to amino acid cellular response to chemical stimulus cellular response to xenobiotic stimulus response to xenobiotic stimulus nuclear DNA replication telomere organization cell cycle DNA replication mitotic cell cycle telomere maintenance via semi-conservative replication cellular component organization mitotic telomere maintenance via semi-conservative replication cell cycle cellular component organization or biogenesis cell cycle process chromosome organization telomere maintenance organelle organization mitotic cell cycle process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process gene expression regulation of cellular biosynthetic process negative regulation of biosynthetic process regulation of catalytic activity positive regulation of molecular function regulation of deoxyribonuclease activity regulation of nuclease activity positive regulation of deoxyribonuclease activity positive regulation of nuclease activity positive regulation of catalytic activity regulation of molecular function positive regulation of hydrolase activity regulation of hydrolase activity regulation of transferase activity regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process regulation of DNA-directed DNA polymerase activity positive regulation of DNA-directed DNA polymerase activity positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of transferase activity positive regulation of DNA biosynthetic process regulation of DNA-templated DNA replication positive regulation of cellular biosynthetic process gland development animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration cellular response to oxidative stress cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to inorganic substance response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV base-excision repair, gap-filling base-excision repair response to metal ion response to cadmium ion response to estradiol	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle enzyme activator complex DNA polymerase processivity factor complex male germ cell nucleus germ cell nucleus membrane-enclosed lumen nuclear replication fork nuclear chromosome intracellular organelle lumen organelle lumen replication fork nuclear lumen chromosome, telomeric region chromosomal region PCNA-p21 complex centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton nucleoplasm nuclear periphery nuclear lamina nuclear body replisome
D, E	Ubiquitin	RNA binding binding organic cyclic compound binding nucleic acid binding structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cation binding ion binding RNA binding binding organic cyclic compound binding nucleic acid binding structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cation binding ion binding metal ion binding small molecule binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process 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 cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process translation gene expression macromolecule biosynthetic process biosynthetic process organic substance biosynthetic process cytoplasmic translation cellular process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytoplasm cytosol cell periphery plasma membrane nucleoplasm organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle cytosolic ribosome ribosome preribosome protein-containing complex ribonucleoprotein complex small-subunit processome synapse cell junction endosome membrane endosome mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cytosolic small ribosomal subunit small ribosomal subunit ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P12004	psoriasis ataxia-telangiectasia-like disorder 2 hepatoblastoma adenocarcinoma malignant colon neoplasm granular cell carcinoma Radiation Injuries, Experimental tubular adenocarcinoma focal segmental glomerulosclerosis endometriosis pancreatic intraductal papillary-mucinous neoplasm glioblastoma primitive neuroectodermal tumor pustulosis palmaris et plantaris Sjogren syndrome psoriasis ataxia-telangiectasia-like disorder 2 hepatoblastoma adenocarcinoma malignant colon neoplasm granular cell carcinoma Radiation Injuries, Experimental tubular adenocarcinoma focal segmental glomerulosclerosis endometriosis pancreatic intraductal papillary-mucinous neoplasm glioblastoma primitive neuroectodermal tumor pustulosis palmaris et plantaris Sjogren syndrome large cell medulloblastoma lung cancer astrocytic tumor nasopharyngeal carcinoma colonic neoplasm neurodegenerative disease dermatomyositis ovarian cancer pituitary cancer IgA glomerulonephritis ischemic disease lung adenocarcinoma ataxia-telangiectasia-like disorder malignant glioma atypical teratoid rhabdoid tumor brain cancer medulloblastoma breast cancer cribriform carcinoma non-small cell lung carcinoma ductal breast carcinoma in situ pancreatic intraductal papillary-mucinous carcinoma invasive ductal breast carcinoma juvenile dermatomyositis lung benign neoplasm lymphoplasmacytic lymphoma ataxia-telangiectasia-like disorder 1 benign colon neoplasm myopathy breast carcinoma cribriform carcinoma of breast oligodendroglioma
D, E	Pharos: P62979	acute myeloid leukemia large cell medulloblastoma Diamond-Blackfan anemia lung carcinoma hematopoietic and lymphoid system neoplasm ulcerative colitis

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.