9EBS | pdb_00009ebs

Cryo-EM structure of USP1-UAF1-Ubiquitin in complex with TNG348

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth C]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	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 [auth C]	WD40	e9ebsC1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
B [auth D]	TIP49	e9ebsD01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: TIP49	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C]	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
B [auth D]	PF11816	WDR48/Bun107, ubiquitin-like domain (Ubl_WDR48-Bun107)	WDR48/Bun107, ubiquitin-like domain	This entry represents the ubiquitin-like domain of WDR48 and its homologues. WDR48 (also known as UAF1) is a regulator of deubiquitinating complexes [1-3]. Bun107 is required for the Ubp9 recruitment to septa and cell tips but also for its enzymatic ...	This entry represents the ubiquitin-like domain of WDR48 and its homologues. WDR48 (also known as UAF1) is a regulator of deubiquitinating complexes [1-3]. Bun107 is required for the Ubp9 recruitment to septa and cell tips but also for its enzymatic activity at these specific locations [4].	Domain
B [auth D]	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	Ubiquitin	protein tag activity molecular tag activity RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule 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	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle cytosolic ribosome membraneless organelle intracellular membraneless organelle ribosome cytosol extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B [auth D]	WD repeat-containing protein 48	DNA binding binding nucleic acid binding double-stranded DNA binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity deubiquitinase activator activity peptidase activator activity protein binding ubiquitin binding ubiquitin-like protein binding DNA binding binding nucleic acid binding double-stranded DNA binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity deubiquitinase activator activity peptidase activator activity protein binding ubiquitin binding ubiquitin-like protein binding single-stranded DNA binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process nucleobase-containing compound metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress recombinational repair positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination positive regulation of cellular process DNA repair positive regulation of DNA recombination double-strand break repair regulation of biological process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of double-strand break repair regulation of DNA repair regulation of double-strand break repair via homologous recombination positive regulation of DNA metabolic process regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process positive regulation of cell communication cell surface receptor signaling pathway via STAT positive regulation of signal transduction signaling positive regulation of receptor signaling pathway via STAT regulation of signal transduction positive regulation of receptor signaling pathway via JAK-STAT cell communication regulation of receptor signaling pathway via JAK-STAT signal transduction regulation of signaling cell surface receptor signaling pathway regulation of cell communication regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT positive regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of Wnt signaling pathway	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome vesicle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen lytic vacuole vacuole lysosome
C [auth E]	Ubiquitin carboxyl-terminal hydrolase 1	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cysteine-type endopeptidase activity endopeptidase activity	regulation of protein stability biological regulation regulation of biological quality response to light stimulus response to stimulus response to radiation response to abiotic stimulus response to UV cellular response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress regulation of protein stability biological regulation regulation of biological quality response to light stimulus response to stimulus response to radiation response to abiotic stimulus response to UV cellular response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair positive regulation of cell communication cell surface receptor signaling pathway via STAT regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process positive regulation of receptor signaling pathway via STAT regulation of signal transduction positive regulation of receptor signaling pathway via JAK-STAT cell communication positive regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT signal transduction positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of response to stimulus regulation of cell communication regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT positive regulation of signaling protein deubiquitination protein modification by small protein removal macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal monoubiquitinated protein deubiquitination regulation of cellular response to stress DNA damage tolerance regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process translesion synthesis DNA synthesis involved in DNA replication DNA replication biosynthetic process positive regulation of DNA metabolic process regulation of macromolecule biosynthetic process error-prone translesion synthesis regulation of metabolic process DNA biosynthetic process regulation of DNA metabolic process positive regulation of error-prone translesion synthesis nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of response to stress regulation of biosynthetic process regulation of error-prone translesion synthesis positive regulation of DNA biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process proteolysis regulation of DNA repair	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C]	IPR019954	Ubiquitin conserved site	Conserved Site
A [auth C]	IPR000626	Ubiquitin-like domain	Domain
A [auth C]	IPR019956	Ubiquitin domain	Domain
A [auth C]	IPR050158	Ubiquitin and ubiquitin-like	Family
A [auth C]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth D]	IPR019775	WD40 repeat, conserved site	Conserved Site
B [auth D]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B [auth D]	IPR051246	WD repeat-containing protein 48	Family
B [auth D]	IPR021772	WDR48/Bun107, ubiquitin-like domain	Domain
B [auth D]	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
B [auth D]	IPR001680	WD40 repeat	Repeat
B [auth D]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C [auth E]	IPR033815	Ubiquitin specific peptidase 1	Domain
C [auth E]	IPR050164	Ubiquitin carboxyl-terminal hydrolases	Family
C [auth E]	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
C [auth E]	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
C [auth E]	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
C [auth E]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C]	: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer
B [auth D]	: Q8TAF3	malignant mesothelioma osteosarcoma Spastic Paraplegia, Hereditary medulloblastoma ovarian cancer metabolic syndrome X psoriasis
C [auth E]	: O94782	amyotrophic lateral sclerosis dermatomyositis large cell medulloblastoma malignant glioma metabolic syndrome X osteosarcoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor glioblastoma lung cancer malignant mesothelioma myopathy ovarian cancer psoriasis breast cancer amyotrophic lateral sclerosis dermatomyositis large cell medulloblastoma malignant glioma metabolic syndrome X osteosarcoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor glioblastoma lung cancer malignant mesothelioma myopathy ovarian cancer psoriasis breast cancer juvenile dermatomyositis lymphoplasmacytic lymphoma medulloblastoma non-alcoholic fatty liver disease Pick disease

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.