4APF | pdb_00004apf

Crystal structure of the human KLHL11-Cul3 complex at 3.1A resolution

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	d4apfb_	All alpha proteins	alpha-alpha superhelix	Cullin repeat-like	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	Cullin repeat-like	8084778	3000059	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	BACK	e4apfA3	A: alpha superhelices	X: Repetitive alpha hairpins	H: BACK domain (From Topology)	T: BACK domain	F: BACK	ECOD (1.6)
A	BTB	e4apfA1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: BTB	ECOD (1.6)
B	Cullin_1st	e4apfB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Cullin_1st	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)
A	1.25.40.420	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	1.20.1310.10	Mainly Alpha	Up-down Bundle	5 helical Cullin repeat like	Cullin Repeats	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07707	BTB And C-terminal Kelch (BACK)	BTB And C-terminal Kelch	This domain is found associated with Pfam:PF00651 and Pfam:PF01344 [1]. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues [1]. This family appears to be closely related to the BTB domain (Finn RD, ...	This domain is found associated with Pfam:PF00651 and Pfam:PF01344 [1]. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues [1]. This family appears to be closely related to the BTB domain (Finn RD, personal observation).	Domain
A	PF00651	BTB/POZ domain (BTB)	BTB/POZ domain	The BTB (for BR-C, ttk and bab) [1] or POZ (for Pox virus and Zinc finger) [2] domain is present near the N-terminus of a fraction of zinc finger (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family o ...	The BTB (for BR-C, ttk and bab) [1] or POZ (for Pox virus and Zinc finger) [2] domain is present near the N-terminus of a fraction of zinc finger (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation [2]. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule [3]. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [4,5,6]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.	Domain
B	PF00888	Cullin family (Cullin)	Cullin family	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	KELCH-LIKE PROTEIN 11	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	catabolic process proteolysis involved in protein catabolic process primary metabolic 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 ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic 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 ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex Cul3-RING ubiquitin ligase complex intracellular protein-containing complex
B	CULLIN 3	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding signaling receptor binding Notch binding 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 ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding signaling receptor binding Notch binding 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 ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding POZ domain binding protein domain specific binding identical protein binding cyclin binding	cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein cellular response to stress modification-dependent macromolecule catabolic process proteolysis response to stress protein metabolic process cellular response to topologically incorrect protein cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein cellular response to stress modification-dependent macromolecule catabolic process proteolysis response to stress protein metabolic process cellular response to topologically incorrect protein primary metabolic process proteasomal protein catabolic process protein catabolic process nuclear protein quality control by the ubiquitin-proteasome system modification-dependent protein catabolic process response to topologically incorrect protein ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins developmental process multicellular organism development multicellular organismal process embryonic cleavage anatomical structure development cell division embryo development gland development animal organ development liver development anatomical structure morphogenesis gland morphogenesis hepaticobiliary system development animal organ morphogenesis liver morphogenesis system development regulation of cellular process negative regulation of biological process negative regulation of type I interferon production cytokine production negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process type I interferon production negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production regulation of cytokinesis positive regulation of cell division regulation of cell cycle process positive regulation of biological process cytokinesis positive regulation of cell cycle regulation of cell division positive regulation of cytokinesis positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process protein destabilization regulation of protein stability regulation of biological quality anaphase-promoting complex-dependent catabolic process establishment of organelle localization cellular localization mitotic metaphase chromosome alignment mitotic cell cycle metaphase chromosome alignment cellular component organization localization chromosome localization organelle localization establishment of localization in cell mitotic sister chromatid segregation cellular component organization or biogenesis chromosome segregation mitotic nuclear division organelle fission chromosome organization sister chromatid segregation establishment of localization organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation establishment of chromosome localization vesicle budding from membrane transport vesicle targeting, to, from or within Golgi vesicle-mediated transport vesicle targeting vesicle organization cellular component biogenesis cellular component assembly protein-containing complex assembly vesicle coating vesicle targeting, rough ER to cis-Golgi membrane organization vesicle localization protein-containing complex organization establishment of vesicle localization intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport COPII-coated vesicle budding COPII vesicle coating Golgi vesicle transport regulation of cell cycle phase transition cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of mitotic cell cycle mitotic cell cycle phase transition protein autoubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal actomyosin structure organization actin cytoskeleton organization actin filament organization actin filament bundle organization contractile actin filament bundle assembly actin filament-based process actin filament bundle assembly stress fiber assembly supramolecular fiber organization cytoskeleton organization cell migration cell motility response to oxidative stress cellular response to chemical stimulus response to chemical cellular response to oxidative stress cellular response to chemical stress fibroblast apoptotic process apoptotic process cell death programmed cell death protein polyubiquitination cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid protein K48-linked ubiquitination G1/S transition of mitotic cell cycle cell cycle G1/S phase transition stem cell division RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound regulation of cellular response to insulin stimulus cellular response to oxygen-containing compound cellular response to endogenous stimulus response to hormone regulation of response to stimulus response to insulin cellular response to insulin stimulus cellular response to hormone stimulus protein monoubiquitination kidney development renal system development positive regulation of organelle organization regulation of mitotic nuclear division positive regulation of mitotic nuclear division positive regulation of mitotic metaphase/anaphase transition mitotic sister chromatid separation positive regulation of nuclear division regulation of chromosome organization regulation of organelle organization regulation of chromosome separation regulation of chromosome segregation regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization regulation of mitotic sister chromatid separation positive regulation of cellular component organization regulation of mitotic metaphase/anaphase transition positive regulation of metaphase/anaphase transition of cell cycle chromosome separation regulation of sister chromatid segregation positive regulation of mitotic sister chromatid separation regulation of nuclear division metaphase/anaphase transition of mitotic cell cycle positive regulation of chromosome separation metaphase/anaphase transition of cell cycle signaling intracellular signal transduction cell communication apoptotic signaling pathway signal transduction intrinsic apoptotic signaling pathway regulation protein catabolic process at synapse regulation of catabolic process regulation protein catabolic process at postsynapse embryonic morphogenesis gastrulation integrin-mediated signaling pathway cell surface receptor signaling pathway regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process 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 post-translational protein modification regulation of protein metabolic process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of TORC1 signaling positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling regulation of TORC1 signaling TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of cell communication TORC1 signaling positive regulation of signaling cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation small GTPase-mediated signal transduction negative regulation of Rho protein signal transduction negative regulation of signaling regulation of small GTPase mediated signal transduction negative regulation of intracellular signal transduction Rho protein signal transduction negative regulation of cell communication intracellular signaling cassette negative regulation of response to stimulus negative regulation of small GTPase mediated signal transduction regulation of Rho protein signal transduction negative regulation of signal transduction trophectodermal cell differentiation cellular developmental process chordate embryonic development cell morphogenesis in utero embryonic development blastocyst formation embryo development ending in birth or egg hatching cell differentiation trophectodermal cellular morphogenesis anatomical structure formation involved in morphogenesis blastocyst development Wnt signaling pathway defense response inflammatory response cell projection organization	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane extracellular exosome membrane-bounded organelle extracellular vesicle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle polymeric cytoskeletal fiber spindle microtubule polar microtubule supramolecular fiber microtubule supramolecular polymer supramolecular complex cytoplasm cytosol cell projection cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection synapse cell junction glutamatergic synapse Golgi apparatus intracellular membrane-bounded organelle endomembrane system postsynapse centrosome microtubule organizing center cell periphery plasma membrane mitotic spindle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex Cul3-RING ubiquitin ligase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015915	Kelch-type beta propeller	Homologous Superfamily
A	IPR006652	Kelch repeat type 1	Repeat
A	IPR011705	BTB/Kelch-associated	Domain
A	IPR000210	BTB/POZ domain	Domain
A	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
B	IPR045093	Cullin	Family
B	IPR019559	Cullin protein, neddylation domain	Domain
B	IPR016158	Cullin homology domain	Domain
B	IPR001373	Cullin, N-terminal	Domain
B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B	IPR016157	Cullin, conserved site	Conserved Site
B	IPR036317	Cullin homology domain superfamily	Homologous Superfamily
B	IPR016159	Cullin repeat-like-containing domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NVR0	breast cancer medulloblastoma large cell medulloblastoma osteosarcoma lung carcinoma
B	Pharos: Q13618	pseudohypoaldosteronism type 2E melanoma prostate cancer Neurodevelopmental Disorders pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma anorexia nervosa tuberculosis atypical teratoid rhabdoid tumor cutaneous melanoma intellectual disability malignant ependymoma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm pseudohypoaldosteronism type 2E melanoma prostate cancer Neurodevelopmental Disorders pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma anorexia nervosa tuberculosis atypical teratoid rhabdoid tumor cutaneous melanoma intellectual disability malignant ependymoma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma spina bifida astrocytic tumor autism spectrum disorder epilepsy large cell medulloblastoma malignant glioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor pseudohypoaldosteronism type 2A subependymal giant cell astrocytoma attention deficit hyperactivity disorder, inattentive type breast cancer glioblastoma lung cancer malignant mesothelioma

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.