Annotations: 9KBF

Cryo-EM structure of the SKP1-FBXO3 complex

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)
B [auth C]	SCOP2B Superfamily	MPT63/MPB63-like	8086822	3002065	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	POZ domain	8035033	3000894	SCOP2B (2022-06-29)
A [auth B]	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 [auth B]	Beta-Casp	e9kbfB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C]	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
B [auth C]	PF09346	SMI1 / KNR4 family (SUKH-1) (SMI1_KNR4)	SMI1 / KNR4 family (SUKH-1)	Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation [1][2]. Genome contextual information showed that SMI1 are primary immunity proteins in bacterial toxin systems [3].	Domain
B [auth C]	PF04379	ApaG domain (DUF525)	ApaG domain	-	Family
A [auth B]	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain		Domain
A [auth B]	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	F-box only protein 3	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 transferase activity catalytic activity ubiquitin-protein transferase activity	regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation regulation of inflammatory response response to external stimulus regulation of response to stimulus response to stress regulation of response to stress inflammatory response primary metabolic process protein ubiquitination regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation regulation of inflammatory response response to external stimulus regulation of response to stimulus response to stress regulation of response to stress inflammatory response primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular 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 proteolysis 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 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process biological process involved in interspecies interaction between organisms response to lipid response to other organism response to oxygen-containing compound response to lipopolysaccharide response to biotic stimulus response to bacterium response to chemical response to external biotic stimulus response to molecule of bacterial origin	cellular anatomical structure intracellular anatomical structure cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus cellular anatomical structure intracellular anatomical structure cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
A [auth B]	S-phase kinase-associated protein 1	protein complex scaffold activity ubiquitin ligase complex scaffold activity structural molecule activity ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding protein domain specific binding enzyme regulator activity ubiquitin ligase activator activity enzyme activator activity ubiquitin-protein transferase regulator activity protein complex scaffold activity ubiquitin ligase complex scaffold activity structural molecule activity ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding protein domain specific binding enzyme regulator activity ubiquitin ligase activator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity cullin family protein binding beta-catenin binding F-box domain binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis developmental process neural crest cell differentiation cellular developmental process animal organ development intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis developmental process neural crest cell differentiation cellular developmental process animal organ development mesenchyme development tissue development stem cell differentiation cell differentiation anatomical structure development cellular process mesenchymal cell differentiation microtubule organizing center organization microtubule cytoskeleton organization cellular component organization centrosome duplication organelle organization centrosome cycle microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization cell cycle process regulation of biological process regulation of cellular process regulation of cellular component organization regulation of centrosome cycle regulation of cell cycle process biological regulation regulation of microtubule-based process regulation of centrosome duplication regulation of cell cycle regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death primary 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 cellular response to stimulus DNA damage checkpoint signaling regulation of cell cycle phase transition response to stimulus 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 regulation of signaling 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 response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway regulation of transmembrane receptor protein serine/threonine kinase signaling pathway cellular response to endogenous stimulus BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of BMP signaling pathway cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus response to BMP response to growth factor transforming growth factor beta receptor superfamily signaling pathway protein polyubiquitination multicellular organism development multicellular organismal process limb development appendage development RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process catabolic process macroautophagy autophagy regulation of mitophagy regulation of catabolic process regulation of autophagy regulation of macroautophagy mitophagy regulation of autophagy of mitochondrion process utilizing autophagic mechanism autophagy of mitochondrion protein K48-linked ubiquitination mitotic cell cycle process G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process maintenance of protein location 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 macromolecule localization protein localization to organelle maintenance of protein localization in organelle intracellular protein localization regulation of mitotic cell cycle rhythmic process circadian rhythm regulation of circadian rhythm regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus xenophagy response to biotic stimulus response to external biotic stimulus regulation of xenophagy response to other organism defense response response to external stimulus defense response to other organism developmental growth growth nervous system development cellular component biogenesis cell junction organization cellular component assembly neuromuscular junction development cell junction assembly synaptic assembly at neuromuscular junction synapse organization synapse assembly system development 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 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cilium assembly cilium organization cell projection assembly regulation of defense response regulation of inflammatory response inflammatory response chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression negative regulation of gene expression, epigenetic TOR signaling regulation of TOR signaling	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR036047	F-box-like domain superfamily	Homologous Superfamily
B [auth C]	IPR007474	ApaG domain	Domain
B [auth C]	IPR001810	F-box domain	Domain
B [auth C]	IPR052121	F-box Protein Family Substrate Recognition Components	Family
B [auth C]	IPR018958	Knr4/Smi1-like domain	Domain
B [auth C]	IPR037883	Knr4/Smi1-like domain superfamily	Homologous Superfamily
B [auth C]	IPR036767	ApaG domain superfamily	Homologous Superfamily
A [auth B]	IPR001232	S-phase kinase-associated protein 1-like	Family
A [auth B]	IPR036296	SKP1-like, dimerisation domain superfamily	Homologous Superfamily
A [auth B]	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
A [auth B]	IPR016897	S-phase kinase-associated protein 1	Family
A [auth B]	IPR016073	SKP1 component, POZ domain	Domain
A [auth B]	IPR016072	SKP1 component, dimerisation	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C]	: Q9UK99	astrocytic tumor Duchenne muscular dystrophy large cell medulloblastoma malignant mesothelioma ovarian cancer spina bifida atypical teratoid rhabdoid tumor glioblastoma limb-girdle muscular dystrophy myopathy pancreatic intraductal papillary-mucinous neoplasm tuberculosis breast cancer hereditary spastic paraplegia malignant glioma astrocytic tumor Duchenne muscular dystrophy large cell medulloblastoma malignant mesothelioma ovarian cancer spina bifida atypical teratoid rhabdoid tumor glioblastoma limb-girdle muscular dystrophy myopathy pancreatic intraductal papillary-mucinous neoplasm tuberculosis breast cancer hereditary spastic paraplegia malignant glioma oligodendroglioma pilocytic astrocytoma
A [auth B]	: 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

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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.