3DOW

Complex structure of GABA type A receptor associated protein and its binding epitope on calreticulin

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3dowa1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	GABA(A) receptor associated protein GABARAP	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3dowa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Atg8	e3dowA1	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 (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
B	PF00262	Calreticulin family (Calreticulin)	Calreticulin family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Gamma-aminobutyric acid receptor-associated protein	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	cellular response to stimulus regulation of biological process regulation of signaling small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction biological regulation regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction cellular response to stimulus regulation of biological process regulation of signaling small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction biological regulation 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 cellular process signal transduction 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 catabolic process organelle assembly vacuole organization macroautophagy cellular metabolic process autophagy autophagosome organization cellular component biogenesis cellular component organization cellular catabolic process organelle organization cellular component assembly metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport transport organic substance transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization positive regulation of protein K48-linked ubiquitination regulation of protein K48-linked ubiquitination regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological 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 organic substance metabolic 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 organonitrogen compound metabolic process 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 organonitrogen compound catabolic process 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 organic substance 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 protein targeting trans-synaptic signaling synaptic signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission microtubule cytoskeleton organization microtubule-based process cytoskeleton organization	membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium cellular anatomical entity cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium cellular anatomical entity cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle intracellular non-membrane-bounded organelle cytoplasm non-membrane-bounded organelle actin cytoskeleton cytosol cell periphery plasma membrane membrane endoplasmic reticulum smooth endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system 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 organelle membrane Golgi membrane Golgi apparatus synapse cell junction protein-containing complex microtubule associated complex microtubule cytoskeleton polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex
B	CRT peptide	complement component C1q complex binding opsonin binding protein-containing complex binding protein binding binding complement binding protein-folding chaperone binding DNA binding organic cyclic compound binding nucleic acid binding RNA binding mRNA binding cation binding transition metal ion binding complement component C1q complex binding opsonin binding protein-containing complex binding protein binding binding complement binding protein-folding chaperone binding DNA binding organic cyclic compound binding nucleic acid binding RNA binding mRNA binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding molecular sequestering activity hormone binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding calcium ion binding nucleocytoplasmic carrier activity nuclear export signal receptor activity molecular carrier activity carbohydrate binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear androgen receptor binding cell adhesion molecule binding integrin binding signaling receptor binding unfolded protein binding peptide binding protein folding chaperone zinc ion binding	multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation response to stimulus response to chemical response to xenobiotic stimulus spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular response to stimulus cellular response to inorganic substance cellular response to metal ion cellular response to lithium ion response to inorganic substance cellular response to chemical stimulus response to lithium ion response to metal ion regulation of protein stability regulation of biological quality protein stabilization protein localization cellular localization establishment of protein localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport organic substance transport intracellular transport protein export from nucleus establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization nuclear export intracellular protein transport organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process protein metabolic process macromolecule metabolic process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process sequestering of calcium ion calcium ion homeostasis maintenance of location in cell maintenance of location cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of cellular biosynthetic process response to organic substance response to ketone response to lipid response to oxygen-containing compound response to testosterone response to organic cyclic compound heart development cardiac muscle tissue development cardiac muscle cell differentiation animal organ development muscle cell differentiation tissue development cardiocyte differentiation striated muscle tissue development circulatory system development muscle structure development striated muscle cell differentiation muscle tissue development regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization vesicle-mediated transport cellular component organization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport endocytosis positive regulation of substrate adhesion-dependent cell spreading regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion substrate adhesion-dependent cell spreading cellular response to stress response to stress cellular senescence RNA metabolic process regulation of primary 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 RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription organelle organization actin cytoskeleton organization cortical actin cytoskeleton organization cortical cytoskeleton organization actin filament-based process cytoskeleton organization intracellular receptor signaling pathway negative regulation of signaling signaling regulation of signal transduction hormone-mediated signaling pathway negative regulation of cell communication cell communication negative regulation of intracellular steroid hormone receptor signaling pathway cellular response to endogenous stimulus response to hormone response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway signal transduction cellular response to organic substance cellular response to steroid hormone stimulus cellular response to hormone stimulus regulation of signaling negative regulation of response to stimulus response to endogenous stimulus cellular response to organic cyclic compound negative regulation of signal transduction steroid hormone mediated signaling pathway regulation of response to stimulus cellular response to lipid nuclear receptor signaling pathway regulation of cell communication intracellular steroid hormone receptor signaling pathway regulation of retinoic acid receptor signaling pathway negative regulation of retinoic acid receptor signaling pathway retinoic acid receptor signaling pathway protein maturation by protein folding peptide antigen assembly with MHC class I protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class I protein complex assembly cellular component biogenesis antigen processing and presentation cellular component assembly immune system process protein-containing complex assembly antigen processing and presentation of peptide antigen via MHC class I MHC protein complex assembly antigen processing and presentation of peptide antigen response to electrical stimulus cellular response to electrical stimulus response to abiotic stimulus cellular response to abiotic stimulus cellular response to environmental stimulus negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process regulation of reproductive process meiotic cell cycle process meiotic nuclear division cell cycle regulation of cell cycle cell cycle process regulation of meiotic cell cycle regulation of cell cycle process meiotic cell cycle organelle fission regulation of organelle organization regulation of meiotic nuclear division nuclear division regulation of nuclear division positive regulation of cell cycle organonitrogen compound biosynthetic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of protein metabolic process regulation of protein metabolic process translation negative regulation of gene expression regulation of translation positive regulation of locomotion regulation of cell motility endothelial cell migration positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration cell migration regulation of multicellular organismal process epithelial cell migration cell motility regulation of epithelial cell migration locomotion epithelium migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of dendritic cell chemotaxis regulation of response to external stimulus dendritic cell chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus taxis positive regulation of mononuclear cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process cell chemotaxis chemotaxis regulation of dendritic cell chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration response to external stimulus positive regulation of leukocyte migration positive regulation of leukocyte chemotaxis regulation of chemotaxis leukocyte migration dendritic cell migration mononuclear cell migration leukocyte chemotaxis protein folding in endoplasmic reticulum intracellular corticosteroid receptor signaling pathway intracellular glucocorticoid receptor signaling pathway cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation multi-multicellular organism process negative regulation of locomotion regulation of trophoblast cell migration female pregnancy embryo implantation negative regulation of trophoblast cell migration negative regulation of cell migration trophoblast cell migration negative regulation of reproductive process negative regulation of cell motility negative regulation of multicellular organismal process multi-organism reproductive process positive regulation of cell communication positive regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction positive regulation of non-canonical NF-kappaB signal transduction positive regulation of signaling response to glycoside protein localization to organelle protein localization to nucleus response to estradiol cellular response to virus biological process involved in interspecies interaction between organisms response to other organism response to external biotic stimulus response to virus response to biotic stimulus	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system lytic vacuole cytolytic granule vacuole cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle extracellular matrix external encapsulating structure collagen-containing extracellular matrix cytosol endoplasmic reticulum smooth endoplasmic reticulum membrane-enclosed lumen sarcoplasmic reticulum lumen intracellular organelle lumen endoplasmic reticulum lumen sarcoplasm organelle lumen sarcoplasmic reticulum intracellular vesicle phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane organelle membrane endocytic vesicle endoplasmic reticulum quality control compartment endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment protein-containing complex MHC class I peptide loading complex organelle subcompartment membrane protein complex endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane perinuclear region of cytoplasm acrosomal vesicle secretory granule secretory vesicle anchoring junction cell junction focal adhesion cell-substrate junction cortical granule intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle lumenal side of endoplasmic reticulum membrane lumenal side of membrane endocytic vesicle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
B	IPR009169	Calreticulin	Family
B	IPR001580	Calreticulin/calnexin	Family
B	IPR018124	Calreticulin/calnexin, conserved site	Conserved Site
B	IPR009033	Calreticulin/calnexin, P domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O95166	Hashimoto thyroiditis vascular disease hypothyroidism schizophrenia
B	Pharos: P27797	essential thrombocythemia primary myelofibrosis esophageal squamous cell carcinoma Melanoma, Experimental myelofibrosis bipolar disorder prostate cancer colorectal cancer thrombocythemia 1 juvenile dermatomyositis ulcerative colitis malignant glioma aleukemic leukemia myelodysplastic syndrome Becker muscular dystrophy essential thrombocythemia primary myelofibrosis esophageal squamous cell carcinoma Melanoma, Experimental myelofibrosis bipolar disorder prostate cancer colorectal cancer thrombocythemia 1 juvenile dermatomyositis ulcerative colitis malignant glioma aleukemic leukemia myelodysplastic syndrome Becker muscular dystrophy myocardial ischemia bone marrow neoplasm cancer pancreatic ductal adenocarcinoma colorectal carcinoma coronary artery disease psoriasis Emery-Dreifuss muscular dystrophy schizoaffective disorder glioblastoma thrombocytosis disease large cell medulloblastoma medulloblastoma astrocytic tumor myopathy breast cancer osteosarcoma chromosome 19p13.13 deletion syndrome paranoid schizophrenia hematopoietic and lymphoid system neoplasm malignant ependymoma atypical teratoid rhabdoid tumor myeloproliferative neoplasm bone marrow disease breast carcinoma ovarian cancer pilocytic astrocytoma congenital anemia Duchenne muscular dystrophy

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.