6O60 | pdb_00006o60

Crystal structure of GGTase3-FBXL2-SKP1 complex

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)
D	d6o60d2	All alpha proteins	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6o60d1	Alpha and beta proteins (a+b)	POZ domain	POZ domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6o60b_	All alpha proteins	alpha/alpha toroid	Terpenoid cyclases/Protein prenyltransferases	Protein prenyltransferases	Rab geranylgeranyltransferase, beta subunit	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)
D	SCOP2B Superfamily	Skp1 dimerisation domain-like	8038683	3000564	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	POZ domain	8035033	3000894	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Terpenoid cyclases/Protein prenyltransferases	8094327	3001024	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	FIVAR	e6o60D1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: FIVAR	ECOD (v294.1)
C	FIVAR	e6o60C1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: FIVAR	ECOD (v294.1)
B	Prenyltrans	e6o60B1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Prenyltrans	ECOD (v294.1)
A		e6o60A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (utative)
B	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation domain		Domain
D	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain		Domain
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
C	PF25372	F-box/LRR-repeat protein 15, leucine rich repeat domain (LRR_FBXL15)	F-box/LRR-repeat protein 15, leucine rich repeat domain	-	Repeat
B	PF00432	Prenyltransferase alpha-alpha toroid domain (Prenyltrans)	Prenyltransferase alpha-alpha toroid domain	-	Repeat
A	PF01239	Protein prenyltransferase alpha subunit repeat (PPTA)	Protein prenyltransferase alpha subunit repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	S-phase kinase-associated protein 1	protein complex scaffold activity ubiquitin ligase complex scaffold activity structural molecule 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 protein complex scaffold activity ubiquitin ligase complex scaffold activity structural molecule 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 ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity beta-catenin binding F-box domain binding	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 cellular process maintenance of protein localization in organelle intracellular protein localization primary 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 cellular process maintenance of protein localization in organelle intracellular protein localization 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 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 protein polyubiquitination protein K48-linked ubiquitination protein monoubiquitination cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex centrosome microtubule organizing center cytoskeleton membraneless organelle membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton 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
C	F-box/LRR-repeat protein 2	protein binding binding calmodulin binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity phosphatidylinositol 3-kinase binding phosphatidylinositol 3-kinase regulatory subunit binding protein phosphatase binding phosphatase binding enzyme binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process 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 macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process 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 cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway regulation of NLRP3 inflammasome complex assembly negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication cellular component biogenesis immune response-activating signaling pathway cellular component assembly inflammasome-mediated signaling pathway positive regulation of immune response canonical inflammasome complex assembly regulation of immune system process signal transduction negative regulation of NLRP3 inflammasome complex assembly positive regulation of immune system process innate immune response-activating signaling pathway negative regulation of cellular component organization immune response response to other organism regulation of innate immune response regulation of inflammasome-mediated signaling pathway negative regulation of protein-containing complex assembly defense response to other organism regulation of pattern recognition receptor signaling pathway NLRP3 inflammasome complex assembly positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular component organization intracellular receptor signaling pathway signaling negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction positive regulation of biological process regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication positive regulation of response to stimulus cellular component organization regulation of protein-containing complex assembly positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction innate immune response negative regulation of cellular process protein-containing complex assembly response to external biotic stimulus cellular component organization or biogenesis regulation of signaling positive regulation of innate immune response negative regulation of response to stimulus protein-containing complex organization defense response to symbiont regulation of cellular component biogenesis negative regulation of signal transduction negative regulation of immune system process immune system process regulation of cell communication negative regulation of inflammasome-mediated signaling pathway catabolic process autophagy regulation of catabolic process regulation of autophagy process utilizing autophagic mechanism regulation of metabolic process protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal protein monoubiquitination proteolysis 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 regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction RNA metabolic process viral life cycle host-mediated perturbation of viral process nucleobase-containing compound biosynthetic process host-mediated perturbation of viral RNA genome replication macromolecule biosynthetic process nucleic acid metabolic process host-mediated perturbation of symbiont process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process modulation of process of another organism	cellular anatomical structure membrane 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
B	Geranylgeranyl transferase type-2 subunit beta	small GTPase binding protein binding binding enzyme binding GTPase binding catalytic activity, acting on a protein protein geranylgeranyltransferase activity protein prenyltransferase activity Rab geranylgeranyltransferase activity prenyltransferase activity transferase activity catalytic activity transferase activity, transferring alkyl or aryl (other than methyl) groups cation binding small GTPase binding protein binding binding enzyme binding GTPase binding catalytic activity, acting on a protein protein geranylgeranyltransferase activity protein prenyltransferase activity Rab geranylgeranyltransferase activity prenyltransferase activity transferase activity catalytic activity transferase activity, transferring alkyl or aryl (other than methyl) groups cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception cellular localization macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception cellular localization transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization vesicle-mediated transport localization intercellular transport establishment of localization in cell Golgi vesicle transport protein prenylation protein geranylgeranylation prenylation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein-containing complex catalytic complex Rab-protein geranylgeranyltransferase complex transferase complex
A	Protein prenyltransferase alpha subunit repeat-containing protein 1	catalytic activity, acting on a protein protein prenyltransferase activity prenyltransferase activity transferase activity catalytic activity transferase activity, transferring alkyl or aryl (other than methyl) groups	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle

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
C	IPR001810	F-box domain	Domain
C	IPR057207	F-box/LRR-repeat protein 15-like, leucin rich repeat domain	Domain
C	IPR050648	F-box/Leucine-rich repeat	Family
C	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C	IPR006553	Leucine-rich repeat, cysteine-containing subtype	Repeat
B	IPR045089	Prenyltransferase subunit beta	Family
B	IPR026873	Geranylgeranyl transferase type-2 subunit beta	Family
B	IPR008930	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Homologous Superfamily
B	IPR001330	Prenyltransferase alpha-alpha toroid domain	Domain
A	IPR002088	Protein prenyltransferase, alpha subunit	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	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
C	Pharos: Q9UKC9	astrocytic tumor lung carcinoma medulloblastoma Pick disease colorectal cancer malignant glioma oligodendroglioma glioblastoma malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia
B	Pharos: P53611	atypical teratoid rhabdoid tumor lung cancer ovarian cancer breast cancer medulloblastoma plasma cell myeloma dermatomyositis myopathy psoriasis
A	Pharos: Q7Z6K3	adrenal cortex carcinoma myopathy pancreatic intraductal papillary-mucinous carcinoma atypical teratoid rhabdoid tumor osteosarcoma pancreatic intraductal papillary-mucinous neoplasm malignant ependymoma ovarian cancer

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.