4WY4 | pdb_00004wy4

Crystal structure of autophagic SNARE 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
Membrane Protein Annotation: OPM

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4wy4b_	Coiled coil proteins	Parallel coiled-coil	SNARE fusion complex	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4wy4a_	Coiled coil proteins	Parallel coiled-coil	SNARE fusion complex	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)
D	SCOP2 Family	SNARE fusion complex	8082566	4003812	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	SNARE fusion complex	8082567	3001549	SCOP2 (2022-06-29)
B	SCOP2 Family	SNARE fusion complex	8067011	4003812	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	SNARE fusion complex	8067012	3001549	SCOP2 (2022-06-29)
A	SCOP2 Family	SNARE fusion complex	8079904	4003812	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SNARE fusion complex	8079905	3001549	SCOP2 (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	Synaptobrevin	e4wy4A1	A: extended segments	X: Synaptobrevin (From Topology)	H: Synaptobrevin (From Topology)	T: Synaptobrevin	F: Synaptobrevin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.5.110	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	1.20.5.110	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.20.5.110	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	1.20.5.110	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00957	Synaptobrevin (Synaptobrevin)	Synaptobrevin	The entry represents the entire v-SNARE coiled-coil homology domain. The process of vesicular membrane fusion in eukaryotic cells depends on a conserved fusion machinery called SNARE (soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein ...	The entry represents the entire v-SNARE coiled-coil homology domain. The process of vesicular membrane fusion in eukaryotic cells depends on a conserved fusion machinery called SNARE (soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors). In the process of vesicle docking, proteins present on the vesicle (v-SNARE) have to bind to their counterpart on the target membrane (t-SNARE) to form a core complex that can then recruit the soluble proteins NSF and SNAP This so called fusion complex can then disassemble after ATP hydrolysis mediated by the ATPase NSF in a process that leads to membrane fusion and the release of the vesicle contents. v-SNAREs include proteins homologous to synaptobrevi [1, 2, 3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	Synaptosomal-associated protein 29	protein binding binding SNARE binding syntaxin binding SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity	membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly autophagosome maturation metabolic process process utilizing autophagic mechanism membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly autophagosome maturation metabolic process process utilizing autophagic mechanism localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization membrane docking organelle localization by membrane tethering organelle localization autophagosome membrane docking cellular localization regulated exocytosis signaling organelle membrane fusion synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport cell communication vesicle-mediated transport in synapse vesicle organization synaptic signaling secretion by cell signal release establishment of localization in cell endomembrane system organization vesicle fusion to plasma membrane trans-synaptic signaling regulation of biological process neurotransmitter secretion secretion biological regulation export from cell cell-cell signaling synaptic vesicle fusion to presynaptic active zone membrane neurotransmitter transport chemical synaptic transmission organelle fusion signal release from synapse organelle organization exocytosis anterograde trans-synaptic signaling synaptic vesicle membrane organization exocytic process vesicle fusion synaptic vesicle priming cellular component biogenesis cellular component assembly protein-containing complex assembly vesicle localization establishment of organelle localization establishment of vesicle localization vesicle targeting organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cilium assembly cilium organization cell projection assembly	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vacuole autophagosome vacuolar membrane autophagosome membrane membrane bounding membrane of organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vacuole autophagosome vacuolar membrane autophagosome membrane membrane bounding membrane of organelle organelle membrane Golgi membrane Golgi apparatus endomembrane system centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton intracellular vesicle lytic vacuole vesicle membrane cytoplasmic vesicle vesicle lysosome azurophil granule lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane secretory granule membrane cytosol SNARE complex protein-containing complex membrane protein complex cell periphery plasma membrane cilium ciliary membrane ciliary pocket membrane plasma membrane bounded cell projection ciliary pocket cell projection plasma membrane region cell projection membrane presynapse synapse cell junction
C	Synaptosomal-associated protein 29	protein binding binding SNARE binding syntaxin binding SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity	membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly autophagosome maturation metabolic process process utilizing autophagic mechanism membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly autophagosome maturation metabolic process process utilizing autophagic mechanism localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization membrane docking organelle localization by membrane tethering organelle localization autophagosome membrane docking cellular localization regulated exocytosis signaling organelle membrane fusion synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport cell communication vesicle-mediated transport in synapse vesicle organization synaptic signaling secretion by cell signal release establishment of localization in cell endomembrane system organization vesicle fusion to plasma membrane trans-synaptic signaling regulation of biological process neurotransmitter secretion secretion biological regulation export from cell cell-cell signaling synaptic vesicle fusion to presynaptic active zone membrane neurotransmitter transport chemical synaptic transmission organelle fusion signal release from synapse organelle organization exocytosis anterograde trans-synaptic signaling synaptic vesicle membrane organization exocytic process vesicle fusion synaptic vesicle priming cellular component biogenesis cellular component assembly protein-containing complex assembly vesicle localization establishment of organelle localization establishment of vesicle localization vesicle targeting organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cilium assembly cilium organization cell projection assembly	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vacuole autophagosome vacuolar membrane autophagosome membrane membrane bounding membrane of organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vacuole autophagosome vacuolar membrane autophagosome membrane membrane bounding membrane of organelle organelle membrane Golgi membrane Golgi apparatus endomembrane system centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton intracellular vesicle lytic vacuole vesicle membrane cytoplasmic vesicle vesicle lysosome azurophil granule lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane secretory granule membrane cytosol SNARE complex protein-containing complex membrane protein complex cell periphery plasma membrane cilium ciliary membrane ciliary pocket membrane plasma membrane bounded cell projection ciliary pocket cell projection plasma membrane region cell projection membrane presynapse synapse cell junction
B	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	membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism cellular component disassembly protein-containing complex organization protein-containing complex disassembly autophagosome maturation membrane docking organelle localization by membrane tethering organelle localization autophagosome membrane docking cellular localization establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport Golgi vesicle transport establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein 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 autolysosome lytic vacuole autolysosome membrane lytic vacuole membrane lysosomal membrane secondary lysosome lysosome transport vesicle transport vesicle membrane cytoplasmic vesicle membrane coated vesicle membrane vesicle membrane ER to Golgi transport vesicle membrane
A	Vesicle-associated membrane protein 8	protein binding binding SNARE binding syntaxin binding molecular function inhibitor activity chloride channel inhibitor activity channel regulator activity transporter inhibitor activity ion channel regulator activity ion channel inhibitor activity molecular function regulator activity transporter regulator activity channel inhibitor activity chloride channel regulator activity protein binding binding SNARE binding syntaxin binding molecular function inhibitor activity chloride channel inhibitor activity channel regulator activity transporter inhibitor activity ion channel regulator activity ion channel inhibitor activity molecular function regulator activity transporter regulator activity channel inhibitor activity chloride channel regulator activity SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity	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 organization transport 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 organization transport membrane fusion organelle membrane fusion establishment of localization vesicle-mediated transport cellular component biogenesis vesicle organization organelle fusion localization organelle organization cellular component assembly protein-containing complex assembly SNARE complex assembly vesicle fusion biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization membrane docking organelle localization by membrane tethering organelle localization autophagosome membrane docking regulation of body fluid levels multicellular organismal process secretion by tissue secretion biological regulation mucus secretion body fluid secretion regulation of biological quality regulation of localization regulation of biological process regulation of cellular process regulation of transport negative regulation of biological process export from cell negative regulation of transport regulation of secretion negative regulation of secretion regulation of secretion by cell secretion by cell negative regulation of cellular process negative regulation of secretion by cell protein localization to cell periphery cellular localization regulation of protein localization protein localization to plasma membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization regulation of protein localization to plasma membrane regulation of protein localization to membrane defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus regulated exocytosis regulation of myeloid leukocyte mediated immunity myeloid leukocyte activation establishment of localization in cell regulation of immune system process immune response histamine secretion by mast cell regulation of inflammatory response mast cell degranulation immune effector process histamine secretion involved in inflammatory response exocytosis regulation of response to stimulus positive regulation of defense response inflammatory response histamine production involved in inflammatory response regulation of defense response regulation of hormone secretion regulation of response to external stimulus hormone secretion histamine secretion positive regulation of exocytosis regulation of mast cell degranulation regulation of regulated secretory pathway positive regulation of response to external stimulus signal release regulation of response to stress leukocyte activation involved in immune response histamine transport positive regulation of immune effector process positive regulation of cellular process production of molecular mediator involved in inflammatory response regulation of signaling cell activation cell-cell signaling regulation of vesicle-mediated transport myeloid cell activation involved in immune response regulation of histamine secretion by mast cell positive regulation of transport immune system process regulation of cell communication exocytic process establishment of organelle localization positive regulation of cell communication regulation of immune effector process positive regulation of histamine secretion by mast cell cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity cell communication positive regulation of leukocyte degranulation positive regulation of regulated secretory pathway positive regulation of inflammatory response leukocyte mediated immunity positive regulation of mast cell degranulation positive regulation of immune system process regulation of hormone levels vacuolar localization regulation of leukocyte mediated immunity lysosome localization positive regulation of multicellular organismal process signaling positive regulation of biological process positive regulation of secretion by cell leukocyte activation positive regulation of response to stimulus positive regulation of hormone secretion positive regulation of secretion mast cell activation regulation of multicellular organismal process regulation of leukocyte degranulation mast cell mediated immunity mast cell activation involved in immune response regulation of exocytosis hormone transport positive regulation of signaling	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule membrane specific granule clathrin-coated vesicle endocytic vesicle membrane coated vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane clathrin-coated endocytic vesicle coated vesicle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle lytic vacuole lysosome vacuolar membrane azurophil granule vacuole lytic vacuole membrane lysosomal membrane primary lysosome azurophil granule membrane cytosol SNARE complex protein-containing complex membrane protein complex cell periphery plasma membrane endosome membrane endosome late endosome membrane late endosome early endosome mucin granule phagocytic vesicle phagocytic vesicle membrane recycling endosome recycling endosome membrane early endosome membrane perinuclear region of cytoplasm zymogen granule zymogen granule membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR000727	Target SNARE coiled-coil homology domain	Domain
C	IPR000727	Target SNARE coiled-coil homology domain	Domain
B	IPR000727	Target SNARE coiled-coil homology domain	Domain
B	IPR006012	Syntaxin/epimorphin, conserved site	Conserved Site
B	IPR010989	SNARE	Homologous Superfamily
B	IPR028676	Syntaxin-17, SNARE motif	Domain
B	IPR045242	Syntaxin	Family
A	IPR001388	Synaptobrevin-like	Family
A	IPR016444	Synaptobrevin/Vesicle-associated membrane protein	Family
A	IPR042855	v-SNARE, coiled-coil homology domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	Pharos: O95721	CEDNIK syndrome palmoplantar keratosis Liver Cirrhosis, Experimental peripheral neuropathy osteosarcoma pancreatic ductal adenocarcinoma schizophrenia erythrokeratoderma malignant mesothelioma ovarian cancer peripheral nervous system disease testicular germ cell tumor intellectual disability myopathy
C	Pharos: O95721	CEDNIK syndrome palmoplantar keratosis Liver Cirrhosis, Experimental peripheral neuropathy osteosarcoma pancreatic ductal adenocarcinoma schizophrenia erythrokeratoderma malignant mesothelioma ovarian cancer peripheral nervous system disease testicular germ cell tumor intellectual disability myopathy
B	Pharos: P56962	alopecia areata melanoma spina bifida cutaneous melanoma osteosarcoma diabetes mellitus ovarian cancer
A	Pharos: Q9BV40	Mammary Neoplasms, Experimental sarcomatoid carcinoma carcinoma malignant mesothelioma ovarian cancer pituitary cancer adrenal cortex carcinoma astrocytic tumor glioblastoma invasive ductal breast carcinoma lung cancer malignant ependymoma myocardial infarction ovarian carcinoma plasma cell myeloma Mammary Neoplasms, Experimental sarcomatoid carcinoma carcinoma malignant mesothelioma ovarian cancer pituitary cancer adrenal cortex carcinoma astrocytic tumor glioblastoma invasive ductal breast carcinoma lung cancer malignant ependymoma myocardial infarction ovarian carcinoma plasma cell myeloma tuberculosis breast carcinoma Duchenne muscular dystrophy heart disease juvenile dermatomyositis lung carcinoma malignant glioma mammary neoplasms, animal osteosarcoma pilocytic astrocytoma prostate carcinoma undifferentiated carcinoma ductal breast carcinoma in situ IgA glomerulonephritis large cell medulloblastoma lymphoplasmacytic lymphoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Transmembrane	Bitopic proteins	SNARE complex	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.