6O60

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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Terpenoid cyclases/Protein prenyltransferases	8094327	3001024	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Skp1 dimerisation domain-like	8038683	3000564	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	POZ domain	8035033	3000894	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	PF01239	e6o60A1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF01239	ECOD (1.6)
B	PF00432	e6o60B1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: PF00432	ECOD (1.6)
C	F_UNCLASSIFIED	e6o60C2	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF13516	e6o60C1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: PF13516	ECOD (1.6)
C	PF12937	e6o60C3	A: alpha arrays	X: F-box domain (From Topology)	H: F-box domain (From Topology)	T: F-box domain	F: PF12937	ECOD (1.6)
D	PF01466,PF03931	e6o60D1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: PF01466,PF03931	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01239	Protein prenyltransferase alpha subunit repeat (PPTA)	Protein prenyltransferase alpha subunit repeat	-	Repeat
B	PF00432	Prenyltransferase and squalene oxidase repeat (Prenyltrans)	Prenyltransferase and squalene oxidase repeat	-	Repeat
C	PF13516	Leucine Rich repeat (LRR_6)	Leucine Rich repeat	-	Repeat
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	-	intracellular anatomical structure cytoplasm cellular anatomical entity
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	organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic 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 organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic 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 metabolic process protein geranylgeranylation protein prenylation cellular process prenylation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane protein-containing complex catalytic complex polyprenyl diphosphate synthase complex Rab-protein geranylgeranyltransferase complex transferase 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	organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic 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 organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic 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 modulation by host of viral RNA genome replication biological process involved in interspecies interaction between organisms cellular biosynthetic process modulation by host of symbiont process RNA metabolic process viral life cycle modulation by host of viral genome replication biological process involved in symbiotic interaction RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process modulation by host of viral process viral RNA genome replication viral process organic substance biosynthetic process biological process involved in interaction with symbiont cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process viral genome replication biosynthetic process organic cyclic compound biosynthetic process cellular process 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 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 regulation of cellular component organization intracellular receptor signaling pathway signaling negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway 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 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 cellular metabolic process regulation of catabolic process regulation of autophagy cellular catabolic process regulation of cellular catabolic process regulation of metabolic process process utilizing autophagic mechanism protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal protein monoubiquitination proteolysis organonitrogen compound 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 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction	membrane cellular anatomical entity 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
D	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002088	Protein prenyltransferase, alpha subunit	Repeat
B	IPR001330	PFTB repeat	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
C	IPR001611	Leucine-rich repeat	Repeat
C	IPR001810	F-box domain	Domain
C	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C	IPR006553	Leucine-rich repeat, cysteine-containing subtype	Repeat
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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
B	Pharos: P53611	atypical teratoid rhabdoid tumor lung cancer ovarian cancer breast cancer medulloblastoma plasma cell myeloma dermatomyositis myopathy psoriasis
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
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

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.