3L2O

Structure-Based Mechanism of Dimerization-Dependent Ubiquitination by the SCFFbx4 Ubiquitin Ligase

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3l2oa1	Alpha and beta proteins (a+b)	POZ domain	POZ domain	BTB/POZ domain	automated matches	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)
A	SCOP2B Superfamily	POZ domain	8035033	3000894	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Skp1 dimerisation domain-like	8038683	3000564	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	Skp1_POZ	e3l2oA1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: Skp1_POZ	ECOD (1.6)
B	F-box-like_1	e3l2oB2	A: alpha arrays	X: F-box domain (From Topology)	H: F-box domain (From Topology)	T: F-box domain	F: F-box-like_1	ECOD (1.6)
B	UNK_F_TYPE	e3l2oB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)
B	1.20.1280.50	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation domain	-	Domain
A	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain	-	Domain
B	PF00646	F-box domain (F-box)	F-box domain	This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; Pfam:PF00560 and Pfam:PF07 ...	This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; Pfam:PF00560 and Pfam:PF07723) and the WD repeat (Pfam:PF00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression [1-2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	S-phase kinase-associated protein 1	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding protein domain specific binding cullin family protein binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity molecular function activator activity molecular function regulator activity beta-catenin binding F-box domain binding	maintenance of protein location protein localization cellular localization maintenance of protein location in nucleus protein localization to nucleus maintenance of location maintenance of location in cell localization maintenance of protein location in cell cellular macromolecule localization macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle maintenance of protein location protein localization cellular localization maintenance of protein location in nucleus protein localization to nucleus maintenance of location maintenance of location in cell localization maintenance of protein location in cell cellular macromolecule localization macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle organonitrogen compound metabolic process primary metabolic process organic substance metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process regulation of protein modification process regulation of catalytic activity positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination regulation of transferase activity positive regulation of post-translational protein modification regulation of primary metabolic process regulation of ubiquitin protein ligase activity positive regulation of metabolic process positive regulation of molecular function positive regulation of ubiquitin protein ligase activity positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of ubiquitin-protein transferase activity regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process positive regulation of transferase activity regulation of post-translational protein modification regulation of protein metabolic process biological regulation positive regulation of catalytic activity regulation of macromolecule metabolic process positive regulation of ubiquitin-protein transferase activity regulation of molecular function regulation of metabolic process protein polyubiquitination protein K48-linked ubiquitination protein monoubiquitination protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cullin-RING ubiquitin ligase complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul7-RING ubiquitin ligase complex
B	F-box only protein 4	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity identical protein binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	cellular homeostasis homeostatic process protein destabilization regulation of protein stability biological regulation regulation of biological quality cellular response to stimulus response to ionizing radiation response to stimulus cellular response to ionizing radiation response to radiation response to abiotic stimulus cellular process cellular response to radiation cellular homeostasis homeostatic process protein destabilization regulation of protein stability biological regulation regulation of biological quality cellular response to stimulus response to ionizing radiation response to stimulus cellular response to ionizing radiation response to radiation response to abiotic stimulus cellular process cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process organic substance metabolic process protein ubiquitination positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process organonitrogen compound metabolic process regulation of post-translational protein modification regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process cellular metabolic process regulation of cellular metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process organic substance biosynthetic process regulation of macromolecule biosynthetic process DNA damage checkpoint signaling regulation of cell cycle phase transition signaling negative regulation of biological process regulation of cellular response to stress negative regulation of cell cycle cell cycle phase transition regulation of signal transduction intracellular signal transduction cell communication regulation of cell cycle checkpoint cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process regulation of signaling regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling DNA damage response regulation of response to stimulus signal transduction in response to DNA damage regulation of cell communication regulation of DNA damage checkpoint cellular senescence telomere organization chromosome organization DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organic cyclic compound metabolic process organelle organization cellular component organization or biogenesis protein polyubiquitination positive regulation of organelle organization regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening positive regulation of telomere maintenance via telomere lengthening regulation of nucleobase-containing compound metabolic process positive regulation of telomere maintenance positive regulation of nucleobase-containing compound metabolic process regulation of chromosome organization regulation of telomere maintenance via telomere lengthening regulation of organelle organization positive regulation of chromosome organization positive regulation of DNA metabolic process positive regulation of telomere maintenance via telomerase organic cyclic compound biosynthetic process DNA biosynthetic process regulation of DNA metabolic process regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization positive regulation of cellular metabolic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process telomere maintenance via telomerase positive regulation of DNA biosynthetic process nucleobase-containing compound biosynthetic process regulation of telomere maintenance via telomerase positive regulation of cellular biosynthetic process negative regulation of cell population proliferation fibroblast proliferation cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation negative regulation of fibroblast proliferation common myeloid progenitor cell proliferation protein localization regulation of localization cellular localization regulation of protein localization regulation of protein localization to nucleus protein localization to nucleus negative regulation of protein localization to nucleus localization regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization to organelle negative regulation of protein localization regulation of protein polyubiquitination positive regulation of protein polyubiquitination	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016073	SKP1 component, POZ domain	Domain
A	IPR001232	S-phase kinase-associated protein 1-like	Family
A	IPR036296	SKP1-like, dimerisation domain superfamily	Homologous Superfamily
A	IPR016072	SKP1 component, dimerisation	Domain
A	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
A	IPR016897	S-phase kinase-associated protein 1	Family
B	IPR001810	F-box domain	Domain
B	IPR039588	F-box only protein 4	Family
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR036047	F-box-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P63208	allergic rhinitis esophageal adenocarcinoma hypothyroidism medulloblastoma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma ovarian cancer plasma cell myeloma systemic lupus erythematosus breast cancer Hashimoto thyroiditis malignant glioma allergic rhinitis esophageal adenocarcinoma hypothyroidism medulloblastoma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma ovarian cancer plasma cell myeloma systemic lupus erythematosus breast cancer Hashimoto thyroiditis malignant glioma pancreatic ductal adenocarcinoma rheumatoid arthritis
B	Pharos: Q9UKT5	acute myeloid leukemia malignant ependymoma esophageal cancer medulloblastoma glioblastoma ovarian cancer

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.