7BV4 | pdb_00007bv4

Crystal structure of STX17 LIR region in complex with GABARAP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d7bv4a_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	GABA(A) receptor associated protein GABARAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d7bv4b_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	GABA(A) receptor associated protein GABARAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d7bv4e_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	GABA(A) receptor associated protein GABARAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d7bv4g_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	GABA(A) receptor associated protein GABARAP	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)
C [auth B]	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
G	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	e7bv4A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
C [auth B]	Atg8	e7bv4B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
E	Atg8	e7bv4E1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
G	Atg8	e7bv4G1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E, G	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, C [auth B], E, G	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 cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation metabolic process cellular component organization or biogenesis 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 organelle assembly vacuole organization autophagosome organization cellular component biogenesis organelle organization cellular component assembly protein localization establishment of protein localization cellular localization nitrogen compound transport 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 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 cellular process 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 regulation of localization protein localization to synapse regulation of protein localization regulation of neurotransmitter receptor localization to postsynaptic specialization membrane regulation of protein localization to synapse neurotransmitter receptor localization to postsynaptic specialization membrane regulation of biological quality regulation of protein localization to membrane regulation of receptor localization to synapse protein localization to postsynaptic specialization membrane protein localization to cell periphery protein localization to postsynaptic membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane protein-containing complex localization regulation of postsynaptic membrane neurotransmitter receptor levels regulation of cellular localization protein localization to organelle protein localization to postsynapse protein localization to cell junction receptor localization to synapse 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 mitophagy autophagy of mitochondrion	membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membraneless organelle cytoplasm 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 GABA-ergic synapse synapse cell junction cytoplasmic vesicle intracellular vesicle vesicle autophagosome vacuolar membrane autophagosome membrane bounding membrane of organelle organelle membrane Golgi membrane Golgi apparatus protein-containing complex microtubule associated complex microtubule cytoskeleton polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex
B [auth C], D, F, H	Syntaxin-17	SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity protein phosphatase binding phosphatase binding protein binding binding enzyme binding SNARE binding kinase binding protein kinase binding	cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism membrane docking organelle localization by membrane tethering cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism membrane docking organelle localization by membrane tethering localization organelle localization autophagosome membrane docking membrane organization transport membrane fusion organelle membrane fusion establishment of localization vesicle-mediated transport vesicle organization organelle fusion organelle organization vesicle fusion cellular localization establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport Golgi vesicle transport protein localization establishment of protein localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport endoplasmic reticulum-Golgi intermediate compartment organization secretion by cell exocytosis secretion export from cell Golgi organization endomembrane system organization autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis cellular component assembly protein localization to phagophore assembly site vesicle docking	cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site cytosol SNARE complex protein-containing complex cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site cytosol SNARE complex protein-containing complex membrane membrane protein complex cell periphery plasma membrane intracellular vesicle COPII-coated ER to Golgi transport vesicle cytoplasmic vesicle coated vesicle vesicle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane vacuole autophagosome vacuolar membrane autophagosome membrane bounding membrane of organelle smooth endoplasmic reticulum membrane smooth endoplasmic reticulum endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment transport vesicle transport vesicle membrane cytoplasmic vesicle membrane coated vesicle membrane vesicle membrane ER to Golgi transport vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E, G	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A, C [auth B], E, G	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth C], D, F, H	IPR000727	Target SNARE coiled-coil homology domain	Domain
B [auth C], D, F, H	IPR006012	Syntaxin/epimorphin, conserved site	Conserved Site
B [auth C], D, F, H	IPR010989	SNARE	Homologous Superfamily
B [auth C], D, F, H	IPR028676	Syntaxin-17, SNARE motif	Domain
B [auth C], D, F, H	IPR045242	Syntaxin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth B], E, G	Pharos: O95166	Hashimoto thyroiditis vascular disease hypothyroidism schizophrenia
B [auth C], D, F, H	Pharos: P56962	alopecia areata melanoma spina bifida cutaneous melanoma osteosarcoma diabetes mellitus ovarian cancer

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B [auth C], C [auth B], D, E A, B [auth C], C [auth B], D, E, F, G, H	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	SNARE Protein Family	STX17/SNAP29/VAMP8 SNARE complex

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.