2NPS

Crystal Structure of the Early Endosomal SNARE Complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
A	d2npsa_	Coiled coil proteins	Parallel coiled-coil	SNARE fusion complex	automated matches	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d2npsb1	Coiled coil proteins	Parallel coiled-coil	SNARE fusion complex	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d2npsb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SNARE fusion complex	8079900	4003812	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SNARE fusion complex	8079901	3001549	SCOP2 (2022-06-29)
B	SCOP2 Family	SNARE fusion complex	8065293	4003812	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	SNARE fusion complex	8065294	3001549	SCOP2 (2022-06-29)
C	SCOP2 Family	SNARE fusion complex	8067891	4003812	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	SNARE fusion complex	8067892	3001549	SCOP2 (2022-06-29)
D	SCOP2 Family	SNARE fusion complex	8082564	4003812	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	SNARE fusion complex	8082565	3001549	SCOP2 (2022-06-29)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00957	Synaptobrevin (Synaptobrevin)	Synaptobrevin	-	Family
B	PF05739	SNARE domain (SNARE)	SNARE domain	-	Family
C	PF12352	Snare region anchored in the vesicle membrane C-terminus (V-SNARE_C)	Snare region anchored in the vesicle membrane C-terminus	Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion; whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the ves ...	Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion; whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the vesicle Pfam:PF05008.	Domain
D	PF05739	SNARE domain (SNARE)	SNARE domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Vesicle-associated membrane protein 4	-	protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane organic substance transport localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport to the plasma membrane protein transport macromolecule localization cellular process Golgi vesicle transport cellular response to stimulus response to organic substance biological process involved in interspecies interaction between organisms response to stimulus response to type II interferon response to cytokine cellular response to type II interferon response to biotic stimulus response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus cellular response to organic substance immune response response to other organism defense response defense response to symbiont response to external stimulus cellular response to chemical stimulus response to chemical immune system process defense response to other organism synaptic vesicle to endosome fusion intracellular transport endosomal transport synaptic vesicle endosomal processing organelle fusion cellular component organization vesicle organization organelle organization establishment of localization in cell endosome organization cellular component organization or biogenesis endomembrane system organization membrane organization protein-containing complex organization membrane fusion organelle membrane fusion cellular component biogenesis cellular component assembly protein-containing complex assembly SNARE complex assembly vesicle fusion Golgi ribbon formation Golgi organization regulation of localization import into cell regulation of cellular process regulation of cellular component organization synaptic vesicle cycle regulation of synaptic vesicle recycling presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling regulation of synaptic vesicle endocytosis regulation of endocytosis synaptic vesicle endocytosis regulation of biological process regulation of transport biological regulation regulation of vesicle-mediated transport endocytosis endocytic recycling regulation of protein localization regulation of protein localization to membrane regulation of establishment of protein localization regulation of protein localization to cell periphery regulation of protein transport regulation of Golgi to plasma membrane protein transport regulation of cellular localization regulation of protein localization to plasma membrane	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network cytoplasm endosome membrane presynaptic endosome membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network cytoplasm endosome membrane presynaptic endosome membrane synapse intracellular vesicle presynapse bounding membrane of organelle cytoplasmic vesicle vesicle membrane cell junction vesicle endosome membrane cytoplasmic vesicle membrane organelle membrane presynaptic endosome cell surface SNARE complex protein-containing complex membrane protein complex phagocytic vesicle endocytic vesicle
B	Syntaxin 13	SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding SNARE binding	regulation of protein stability biological regulation regulation of biological quality protein stabilization regulation of postsynaptic membrane neurotransmitter receptor levels cellular localization synaptic vesicle to endosome fusion transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport synaptic vesicle endosomal processing organelle fusion regulation of protein stability biological regulation regulation of biological quality protein stabilization regulation of postsynaptic membrane neurotransmitter receptor levels cellular localization synaptic vesicle to endosome fusion transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport synaptic vesicle endosomal processing organelle fusion cellular component organization vesicle organization localization organelle organization establishment of localization in cell endosome organization cellular process cellular component organization or biogenesis endomembrane system organization autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy cellular metabolic process autophagy autophagosome organization cellular component biogenesis cellular catabolic process cellular component assembly metabolic process process utilizing autophagic mechanism membrane organization membrane fusion organelle membrane fusion vesicle fusion protein localization establishment of protein localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport lipid localization lipid transport organic hydroxy compound transport cholesterol transport sterol transport cholesterol efflux localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane organelle localization by membrane tethering organelle localization vesicle docking membrane docking	cellular anatomical entity endomembrane system membrane-bounded organelle organelle vesicle SNARE complex protein-containing complex intracellular anatomical structure membrane membrane protein complex cytoplasm intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle cellular anatomical entity endomembrane system membrane-bounded organelle organelle vesicle SNARE complex protein-containing complex intracellular anatomical structure membrane membrane protein complex cytoplasm intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle endocytic vesicle membrane microdomain membrane raft endosome membrane synapse postsynaptic endosome bounding membrane of organelle vesicle membrane cell junction endosome postsynapse cytoplasmic vesicle membrane postsynaptic endosome membrane organelle membrane recycling endosome recycling endosome membrane postsynaptic recycling endosome Golgi membrane Golgi apparatus early endosome early endosome membrane BLOC complex intracellular protein-containing complex BLOC-1 complex transport vesicle membrane presynapse synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane secretory vesicle exocytic vesicle phagophore assembly site
C	Vesicle transport through interaction with t-SNAREs homolog 1A	SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding SNARE binding	cellular localization post-Golgi vesicle-mediated transport transport intracellular transport establishment of localization vesicle-mediated transport Golgi to vacuole transport localization establishment of localization in cell vacuolar transport cellular process Golgi vesicle transport synaptic vesicle to endosome fusion endosomal transport cellular localization post-Golgi vesicle-mediated transport transport intracellular transport establishment of localization vesicle-mediated transport Golgi to vacuole transport localization establishment of localization in cell vacuolar transport cellular process Golgi vesicle transport synaptic vesicle to endosome fusion endosomal transport synaptic vesicle endosomal processing organelle fusion cellular component organization vesicle organization organelle organization endosome organization cellular component organization or biogenesis endomembrane system organization voluntary musculoskeletal movement multicellular organismal movement musculoskeletal movement multicellular organismal process system process nervous system process neuromuscular process cellular catabolic process catabolic process cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism endoplasmic reticulum to Golgi vesicle-mediated transport intra-Golgi vesicle-mediated transport protein localization establishment of protein localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport macroautophagy cytosolic transport retrograde transport, endosome to Golgi membrane organization membrane fusion organelle membrane fusion vesicle fusion with Golgi apparatus vesicle fusion Golgi organization localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	axon synapse neuron projection cellular anatomical entity axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon terminal bouton cell junction neuron projection terminus membrane-bounded organelle intracellular anatomical structure axon synapse neuron projection cellular anatomical entity axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon terminal bouton cell junction neuron projection terminus membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle clathrin-coated vesicle coated vesicle cytoplasm vesicle cytosol SNARE complex protein-containing complex membrane membrane protein complex endosome membrane endosome late endosome membrane endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane late endosome organelle membrane coated vesicle membrane clathrin-coated vesicle membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuole autophagosome neuron to neuron synapse hippocampal mossy fiber to CA3 synapse Golgi apparatus Golgi membrane perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body transport vesicle membrane synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane secretory vesicle exocytic vesicle COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane
D	Syntaxin-6	protein binding binding SNARE binding syntaxin binding SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity	cellular localization synaptic vesicle to endosome fusion transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport synaptic vesicle endosomal processing organelle fusion cellular component organization vesicle organization localization organelle organization establishment of localization in cell cellular localization synaptic vesicle to endosome fusion transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport synaptic vesicle endosomal processing organelle fusion cellular component organization vesicle organization localization organelle organization establishment of localization in cell endosome organization cellular process cellular component organization or biogenesis endomembrane system organization membrane organization membrane fusion organelle membrane fusion vesicle fusion Golgi vesicle transport protein localization establishment of protein localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport regulation of localization regulation of biological process regulation of cellular process regulation of protein localization biological regulation regulation of cellular localization cytosolic transport retrograde transport, endosome to Golgi localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane organelle localization by membrane tethering organelle localization vesicle docking membrane docking	cellular anatomical entity endomembrane system membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle clathrin-coated vesicle coated vesicle cytoplasm vesicle cytosol cellular anatomical entity endomembrane system membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle clathrin-coated vesicle coated vesicle cytoplasm vesicle cytosol SNARE complex protein-containing complex membrane membrane protein complex phagocytic vesicle endocytic vesicle cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen early endosome endosome endosome membrane recycling endosome cytoplasmic vesicle membrane bounding membrane of organelle recycling endosome membrane vesicle membrane organelle membrane Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network Golgi membrane trans-Golgi network membrane perinuclear region of cytoplasm synapse transport vesicle membrane presynapse synaptic vesicle synaptic vesicle membrane cell junction transport vesicle exocytic vesicle membrane secretory vesicle exocytic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR042887	Vesicle-associated membrane protein 4	Family
A	IPR001388	Synaptobrevin-like	Family
A	IPR042855	v-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	IPR006011	Syntaxin, N-terminal domain	Domain
B	IPR045242	Syntaxin	Family
C	IPR038407	Vesicle transport v-SNARE, N-terminal domain superfamily	Homologous Superfamily
C	IPR000727	Target SNARE coiled-coil homology domain	Domain
C	IPR027027	GOSR2/Membrin/Bos1	Family
C	IPR007705	Vesicle transport v-SNARE, N-terminal	Domain
C	IPR010989	SNARE	Homologous Superfamily
D	IPR000727	Target SNARE coiled-coil homology domain	Domain
D	IPR015260	Syntaxin 6, N-terminal	Domain
D	IPR006012	Syntaxin/epimorphin, conserved site	Conserved Site
D	IPR010989	SNARE	Homologous Superfamily
D	IPR045242	Syntaxin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	Pharos: O43752	progressive supranuclear palsy breast cancer Creutzfeldt Jacob disease invasive ductal breast carcinoma non-small cell lung carcinoma breast carcinoma ductal breast carcinoma in situ medulloblastoma osteosarcoma psoriasis CEROID LIPOFUSCINOSIS, NEURONAL, 6 IgA glomerulonephritis neuronal ceroid lipofuscinosis 6 ovarian cancer tuberculosis

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM				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 R01GM133198.