6HYM

Structure of PCM1 LIR motif bound to GABARAP

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)
A	d6hyma_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6hymb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], 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)
A	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	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	Atg8	e6hymA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
B	Atg8	e6hymB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02991	Autophagy protein Atg8 ubiquitin like (ATG8)	Autophagy protein Atg8 ubiquitin like	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of ...	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Pericentriolar material 1 protein,Gamma-aminobutyric acid receptor-associated protein	molecular adaptor activity identical protein binding protein binding binding signaling receptor binding GABA receptor binding phosphatidylethanolamine binding phospholipid binding lipid binding cytoskeletal protein binding microtubule binding tubulin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding molecular adaptor activity identical protein binding protein binding binding signaling receptor binding GABA receptor binding phosphatidylethanolamine binding phospholipid binding lipid binding cytoskeletal protein binding microtubule binding tubulin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding beta-tubulin binding	protein localization to microtubule cytoskeleton protein localization cellular localization protein localization to microtubule organizing center localization protein localization to cytoskeleton protein localization to organelle cellular macromolecule localization macromolecule localization cellular process protein localization to centrosome cell projection organization transport plasma membrane bounded cell projection assembly protein localization to microtubule cytoskeleton protein localization cellular localization protein localization to microtubule organizing center localization protein localization to cytoskeleton protein localization to organelle cellular macromolecule localization macromolecule localization cellular process protein localization to centrosome cell projection organization transport plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization cellular component assembly establishment of localization in cell cilium assembly transport along microtubule cellular component organization or biogenesis cilium organization intraciliary transport organelle assembly plasma membrane bounded cell projection organization intraciliary transport involved in cilium assembly intracellular transport establishment of localization protein-containing complex localization organelle organization microtubule-based transport cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process cell projection assembly regulation of protein complex stability biological regulation regulation of biological quality microtubule cytoskeleton organization microtubule anchoring cytoskeleton organization non-motile cilium assembly cytoplasmic microtubule organization supramolecular fiber organization protein-containing complex localization to centriolar satellite microtubule organizing center organization centrosome cycle cell cycle cell cycle process behavior multicellular organismal process biological process involved in intraspecies interaction between organisms social behavior regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process cell development regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of nervous system development negative regulation of neurogenesis multicellular organism development neurogenesis cell differentiation anatomical structure development negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development regulation of biological process negative regulation of developmental process nervous system development negative regulation of cell development negative regulation of multicellular organismal process neuron migration generation of neurons cell migration cell motility establishment of organelle localization forebrain development organelle localization nuclear migration cell proliferation in forebrain head development cell population proliferation animal organ development brain development nucleus localization interkinetic nuclear migration central nervous system development neural precursor cell proliferation microtubule anchoring at microtubule organizing center microtubule anchoring at centrosome regulation of localization establishment of protein localization nitrogen compound transport regulation of protein localization positive regulation of biological process positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of intracellular transport positive regulation of cellular process regulation of intracellular transport regulation of transport regulation of establishment of protein localization regulation of protein transport positive regulation of transport protein transport regulation of cellular localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport neuronal stem cell population maintenance maintenance of cell number stem cell population maintenance cellular response to stimulus regulation of signaling small GTPase-mediated signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication signal transduction cellular component disassembly catabolic process macroautophagy protein-containing complex organization cellular metabolic process autophagy protein-containing complex disassembly cellular catabolic process autophagosome maturation metabolic process process utilizing autophagic mechanism response to nutrient levels cellular response to nitrogen levels cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation autophagosome assembly vacuole organization autophagosome organization positive regulation of protein K48-linked ubiquitination regulation of protein K48-linked ubiquitination regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process protein metabolic process protein modification 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 protein polyubiquitination regulation of post-translational protein modification regulation of protein metabolic process protein polyubiquitination primary metabolic process regulation of macromolecule metabolic process positive regulation of protein polyubiquitination macromolecule modification macromolecule metabolic process post-translational protein modification protein modification by small protein conjugation regulation of metabolic process protein K48-linked ubiquitination protein modification by small protein conjugation or removal positive regulation of proteasomal protein catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process extrinsic apoptotic signaling pathway via death domain receptors cell surface receptor signaling pathway cell death extrinsic apoptotic signaling pathway apoptotic signaling pathway apoptotic process programmed cell death autophagy of mitochondrion protein targeting trans-synaptic signaling synaptic signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission	membrane cellular anatomical entity apical part of cell membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane membrane cellular anatomical entity apical part of cell membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane ciliary transition zone cell projection cilium plasma membrane bounded cell projection centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle centriolar satellite centriole cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex pericentriolar material ciliary basal body axoneme ciliary plasm cytoplasmic region plasma membrane bounded cell projection cytoplasm actin cytoskeleton cell periphery plasma membrane endoplasmic reticulum smooth endoplasmic reticulum sperm midpiece 9+2 motile cilium sperm flagellum motile cilium lytic vacuole vacuole lysosome cytoplasmic vesicle intracellular vesicle vesicle autophagosome vacuolar membrane autophagosome membrane bounding membrane of organelle Golgi membrane Golgi apparatus synapse cell junction microtubule associated complex polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR031446	Pericentriolar material 1 protein, C-terminal	Domain
A, B	IPR024138	Pericentriolar material 1 protein	Family
A, B	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A, B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O95166	schizophrenia astrocytic tumor breast cancer hereditary spastic paraplegia lung adenocarcinoma malignant ependymoma psoriasis thyroid gland papillary carcinoma atrial fibrillation breast carcinoma invasive ductal breast carcinoma lung cancer medulloblastoma atypical teratoid rhabdoid tumor cancer schizophrenia astrocytic tumor breast cancer hereditary spastic paraplegia lung adenocarcinoma malignant ependymoma psoriasis thyroid gland papillary carcinoma atrial fibrillation breast carcinoma invasive ductal breast carcinoma lung cancer medulloblastoma atypical teratoid rhabdoid tumor cancer large cell medulloblastoma malignant colon neoplasm ovarian cancer sinusitis Hashimoto thyroiditis vascular disease hypothyroidism schizophrenia

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.