3BW6 | pdb_00003bw6

Crystal structure of the longin domain of yeast Ykt6

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3bw6a1	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Synatpobrevin N-terminal domain	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d3bw6a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SNARE-like	8044561	3001113	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	Longin	e3bw6A1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: Longin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.450.50	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Longin domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13774	Regulated-SNARE-like domain (Longin)	Regulated-SNARE-like domain	Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex [1]. Longins are the only ...	Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex [1]. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterised by a conserved N-terminal domain with a profilin-like fold called a longin domain [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Synaptobrevin homolog YKT6	SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity palmitoyltransferase activity catalytic activity	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 Golgi vesicle fusion to target membrane Golgi vesicle transport vacuole fusion vacuole organization vacuole fusion, non-autophagic cellular localization establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport amphisome-lysosome fusion intra-Golgi vesicle-mediated transport establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization intracellular protein transport vesicle fusion with Golgi apparatus Golgi organization endomembrane system organization Golgi to endosome transport post-Golgi vesicle-mediated transport cytosolic transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle storage vacuole lytic vacuole vacuole fungal-type vacuole membrane Golgi cis cisterna membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle storage vacuole lytic vacuole vacuole fungal-type vacuole membrane Golgi cis cisterna membrane Golgi cisterna membrane Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna endomembrane system Golgi cis cisterna Golgi stack organelle membrane cytosol SNARE complex protein-containing complex membrane protein complex cell periphery plasma membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuolar membrane autophagosome membrane autophagosome bounding membrane of organelle endosome intracellular vesicle cytoplasmic vesicle vesicle Golgi membrane endosome membrane cytoplasmic vesicle membrane vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001388	Synaptobrevin-like	Family
A	IPR045848	YKT6, SNARE motif	Domain
A	IPR011012	Longin-like domain superfamily	Homologous Superfamily
A	IPR010908	Longin domain	Domain
A	IPR042855	v-SNARE, coiled-coil homology domain	Domain

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.