8GRF

Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Skp1 dimerisation domain-like	8043773	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)
D	F_UNCLASSIFIED	e8grfD1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8grfA1	A: alpha complex topology	X: Citrate synthase-like	H: Citrate synthase (From Topology)	T: Citrate synthase	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8grfB1	A: alpha complex topology	X: Citrate synthase-like	H: Citrate synthase (From Topology)	T: Citrate synthase	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain	-	Domain
D	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation domain	-	Domain
A, B	PF00285	Citrate synthase, C-terminal domain (Citrate_synt)	Citrate synthase, C-terminal domain	This is the long, C-terminal part of the enzyme.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	F-box protein UCC1	protein-macromolecule adaptor activity molecular adaptor activity	protein ubiquitination macromolecule modification metabolic process primary 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 catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process protein ubiquitination macromolecule modification metabolic process primary 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 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	cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex
D	E3 ubiquitin ligase complex SCF subunit	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding DNA replication origin binding protein binding cullin family protein binding	regulation of biological process regulation of cellular process regulation of cellular component organization protein-containing complex organization biological regulation regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis cell cycle regulation of biological process regulation of cellular process regulation of cellular component organization protein-containing complex organization biological regulation regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis cell cycle mitotic cell cycle cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process translation gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of cytoplasmic translation negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process cytoplasmic translation metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of cytoplasmic translation regulation of metabolic process regulation of mitotic cell cycle regulation of cell cycle organelle fusion organelle organization mitochondrial fusion mitochondrion organization proton-transporting V-type ATPase complex assembly vacuolar proton-transporting V-type ATPase complex assembly proton-transporting two-sector ATPase complex assembly organelle assembly non-membrane-bounded organelle assembly chromosome organization protein-DNA complex assembly protein-DNA complex organization kinetochore assembly kinetochore organization centromere complex assembly regulation of cell cycle phase transition cell cycle phase transition exit from mitosis cell cycle process mitotic nuclear division regulation of cell cycle process organelle fission regulation of mitotic cell cycle phase transition nuclear division mitotic cell cycle process regulation of exit from mitosis mitotic cell cycle phase transition chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression constitutive heterochromatin formation silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic macromolecule modification post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal protein ubiquitination 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 septin ring organization septin ring assembly septin cytoskeleton organization cytoskeleton organization oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process organic acid metabolic process regulation of sulfur metabolic process regulation of small molecule metabolic process sulfur compound metabolic process small molecule metabolic process regulation of sulfur amino acid metabolic process regulation of localization hexose transmembrane transport regulation of transport transport positive regulation of biological process carbohydrate transport establishment of localization positive regulation of D-glucose transmembrane transport transmembrane transport localization regulation of transmembrane transport positive regulation of transport D-glucose transmembrane transport positive regulation of transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport positive regulation of cellular process subtelomeric heterochromatin formation telomere organization RNA 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 transcription by galactose regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription G1/S transition of mitotic cell cycle cell cycle G1/S phase transition response to stimulus response to chemical cellular response to methylmercury response to methylmercury cellular response to stimulus DNA damage checkpoint signaling signaling negative regulation of cell cycle intracellular signal transduction negative regulation of mitotic cell cycle cell communication mitotic DNA integrity checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition signal transduction mitotic intra-S DNA damage checkpoint signaling DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling DNA damage response signal transduction in response to DNA damage cell cycle G2/M phase transition G2/M transition of mitotic cell cycle homeostatic process intracellular pH reduction regulation of intracellular pH vacuolar acidification cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis regulation of biological quality monoatomic cation homeostasis regulation of cellular pH intracellular monoatomic ion homeostasis	cellular anatomical entity endomembrane system protein-containing complex intracellular anatomical structure cytoplasm RAVE complex membrane-bounded organelle nucleus nuclear protein-containing complex chromosome CBF3 complex intracellular membrane-bounded organelle chromosomal region intracellular organelle cellular anatomical entity endomembrane system protein-containing complex intracellular anatomical structure cytoplasm RAVE complex membrane-bounded organelle nucleus nuclear protein-containing complex chromosome CBF3 complex intracellular membrane-bounded organelle chromosomal region intracellular organelle organelle intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle cullin-RING ubiquitin ligase complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome chromosome, telomeric region
A, B	Citrate synthase	citrate (Si)-synthase activity citrate synthase activity acyltransferase activity acyltransferase activity, acyl groups converted into alkyl on transfer transferase activity catalytic activity identical protein binding protein binding binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process primary metabolic process generation of precursor metabolites and energy carbohydrate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process primary metabolic process generation of precursor metabolites and energy carbohydrate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process organic acid metabolic process citrate metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle peroxisome microbody membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR016073	SKP1 component, POZ domain	Domain
D	IPR001232	S-phase kinase-associated protein 1-like	Family
D	IPR036296	SKP1-like, dimerisation domain superfamily	Homologous Superfamily
D	IPR016072	SKP1 component, dimerisation	Domain
D	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
D	IPR016897	S-phase kinase-associated protein 1	Family
A, B	IPR010109	Citrate synthase, eukaryotic-type	Family
A, B	IPR019810	Citrate synthase active site	Active Site
A, B	IPR016143	Citrate synthase-like, small alpha subdomain	Homologous Superfamily
A, B	IPR036969	Citrate synthase superfamily	Homologous Superfamily
A, B	IPR002020	Citrate synthase	Family
A, B	IPR016142	Citrate synthase-like, large alpha subdomain	Homologous Superfamily

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 R01GM133198.