3PUK

Re-refinement of the crystal structure of Munc18-3 and Syntaxin4 N-peptide complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Sec1/munc18-like	8066433	3001920	SCOP2B (2022-06-29)
A	SCOP2 Family	Sec1/munc18-like (SM) proteins	8066432	4002933	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sec1/munc18-like	8066433	3001920	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)
B	Sec1_3rd	e3pukB7	A: alpha complex topology	X: alpha-helical domain in sec1/munc18-like (SM) proteins (From Topology)	H: alpha-helical domain in sec1/munc18-like (SM) proteins (From Topology)	T: alpha-helical domain in sec1/munc18-like (SM) proteins	F: Sec1_3rd	ECOD (1.6)
B	Sec1_1st_1	e3pukB8	A: a/b three-layered sandwiches	X: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	H: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	T: Rossmann-like domains in Sec1/munc18-like proteins	F: Sec1_1st_1	ECOD (1.6)
B	Sec1_2nd	e3pukB3	A: a/b three-layered sandwiches	X: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	H: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	T: Rossmann-like domains in Sec1/munc18-like proteins	F: Sec1_2nd	ECOD (1.6)
A	Sec1_3rd	e3pukA3	A: alpha complex topology	X: alpha-helical domain in sec1/munc18-like (SM) proteins (From Topology)	H: alpha-helical domain in sec1/munc18-like (SM) proteins (From Topology)	T: alpha-helical domain in sec1/munc18-like (SM) proteins	F: Sec1_3rd	ECOD (1.6)
A	Sec1_1st_1	e3pukA1	A: a/b three-layered sandwiches	X: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	H: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	T: Rossmann-like domains in Sec1/munc18-like proteins	F: Sec1_1st_1	ECOD (1.6)
A	Sec1_2nd	e3pukA4	A: a/b three-layered sandwiches	X: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	H: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	T: Rossmann-like domains in Sec1/munc18-like proteins	F: Sec1_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.2060	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 1	CATH (4.3.0)
B	3.40.50.1910	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 2	CATH (4.3.0)
B	3.90.830.10	Alpha Beta	Alpha-Beta Complex	Syntaxin Binding Protein 1	Chain A, domain 2	CATH (4.3.0)
B	1.25.40.60	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	3.40.50.2060	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 1	CATH (4.3.0)
A	3.40.50.1910	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 2	CATH (4.3.0)
A	3.90.830.10	Alpha Beta	Alpha-Beta Complex	Syntaxin Binding Protein 1	Chain A, domain 2	CATH (4.3.0)
A	1.25.40.60	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00995	Sec1 family (Sec1)	Sec1 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Syntaxin-4 N-terminal peptide	small GTPase binding protein binding binding enzyme binding GTPase binding SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity enzyme regulator activity enzyme activator activity molecular function activator activity phospholipase activator activity molecular function regulator activity lipase activator activity small GTPase binding protein binding binding enzyme binding GTPase binding SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity enzyme regulator activity enzyme activator activity molecular function activator activity phospholipase activator activity molecular function regulator activity lipase activator activity sphingomyelin phosphodiesterase activator activity SNARE binding	membrane organization protein-containing complex organization transport membrane fusion organelle membrane fusion establishment of localization vesicle-mediated transport cellular component organization cellular component biogenesis vesicle organization organelle fusion localization organelle organization cellular component assembly protein-containing complex assembly membrane organization protein-containing complex organization transport membrane fusion organelle membrane fusion establishment of localization vesicle-mediated transport cellular component organization cellular component biogenesis vesicle organization organelle fusion localization organelle organization cellular component assembly protein-containing complex assembly SNARE complex assembly cellular process cellular component organization or biogenesis vesicle fusion positive regulation of protein localization to plasma membrane protein localization regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process cellular macromolecule localization regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery regulation of biological process protein localization to cell periphery protein localization to plasma membrane biological regulation positive regulation of protein localization to membrane localization within membrane regulation of protein localization to cell periphery protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of protein localization to plasma membrane chemotaxis positive regulation of locomotion response to stimulus regulation of response to external stimulus response to external stimulus regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus taxis regulation of response to stimulus response to chemical regulation of locomotion locomotion cellular response to stimulus extrinsic apoptotic signaling pathway via death domain receptors signaling regulation of signal transduction regulation of programmed cell death extrinsic apoptotic signaling pathway cell communication signal transduction regulation of signaling cell surface receptor signaling pathway regulation of apoptotic process cell death regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway via death domain receptors regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway response to oxidative stress cellular response to chemical stimulus cellular response to stress response to stress cellular response to oxidative stress cellular response to chemical stress vesicle-mediated transport in synapse regulation of immune effector process immunoglobulin production cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of immune effector process regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of immune system process positive regulation of immunoglobulin production regulation of biosynthetic process production of molecular mediator of immune response cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of immunoglobulin production positive regulation of gene expression immune system process positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process metabolic process regulation of production of molecular mediator of immune response macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process positive regulation of protein localization to cell surface protein localization to cell surface regulation of protein localization to cell surface cornified envelope assembly membrane biogenesis membrane assembly plasma membrane organization endomembrane system organization regulated exocytosis synaptic vesicle cycle synaptic vesicle exocytosis synaptic signaling secretion by cell signal release establishment of localization in cell trans-synaptic signaling neurotransmitter secretion secretion cell-cell signaling export from cell neurotransmitter transport chemical synaptic transmission signal release from synapse exocytosis anterograde trans-synaptic signaling multicellular organismal process regulation of myeloid leukocyte mediated immunity positive regulation of leukocyte mediated immunity cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity myeloid leukocyte activation positive regulation of leukocyte degranulation positive regulation of immune response positive regulation of regulated secretory pathway leukocyte mediated immunity immune response regulation of secretion regulation of leukocyte mediated immunity positive regulation of myeloid leukocyte mediated immunity eosinophil mediated immunity regulation of immune response eosinophil activation positive regulation of secretion by cell positive regulation of exocytosis leukocyte activation regulation of regulated secretory pathway regulation of eosinophil degranulation regulation of secretion by cell positive regulation of secretion positive regulation of eosinophil degranulation leukocyte activation involved in immune response eosinophil degranulation eosinophil activation involved in immune response regulation of leukocyte degranulation regulation of transport cell activation regulation of vesicle-mediated transport myeloid cell activation involved in immune response positive regulation of transport regulation of exocytosis granulocyte activation organelle localization by membrane tethering organelle localization vesicle docking membrane docking vesicle docking involved in exocytosis synaptic vesicle docking exocytic process cell adhesion positive regulation of cell adhesion regulation of cell adhesion cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation establishment of protein localization nitrogen compound transport organic substance transport intracellular transport protein transport intracellular protein transport positive regulation of cell communication response to organic substance positive regulation of establishment of protein localization carbohydrate homeostasis positive regulation of insulin secretion involved in cellular response to glucose stimulus positive regulation of insulin secretion regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region intracellular glucose homeostasis protein secretion cellular response to oxygen-containing compound regulation of protein secretion cellular response to carbohydrate stimulus chemical homeostasis response to glucose glucose homeostasis insulin secretion involved in cellular response to glucose stimulus regulation of hormone secretion regulation of peptide secretion homeostatic process hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion positive regulation of hormone secretion response to monosaccharide response to carbohydrate amide transport cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus cellular response to organic substance positive regulation of peptide secretion regulation of peptide transport regulation of establishment of protein localization response to oxygen-containing compound cellular response to glucose stimulus regulation of protein transport positive regulation of protein secretion peptide transport response to hexose cellular homeostasis regulation of insulin secretion peptide hormone secretion regulation of insulin secretion involved in cellular response to glucose stimulus hormone transport insulin secretion positive regulation of signaling biological process involved in interspecies interaction between organisms response to type II interferon response to cytokine cellular response to type II interferon response to biotic stimulus innate immune response cellular response to cytokine stimulus response to external biotic stimulus response to other organism defense response defense response to symbiont defense response to other organism regulation of cell motility positive regulation of cell migration positive regulation of cell motility regulation of cell migration cell migration cell motility protein localization to synapse neurotransmitter receptor transport to postsynaptic membrane establishment of protein localization to postsynaptic membrane neurotransmitter receptor transport to plasma membrane protein localization to postsynaptic membrane neurotransmitter receptor transport establishment of protein localization to membrane exocytic insertion of neurotransmitter receptor to postsynaptic membrane protein-containing complex localization vesicle-mediated transport to the plasma membrane regulation of postsynaptic membrane neurotransmitter receptor levels protein localization to postsynapse protein localization to cell junction receptor localization to synapse modulation of chemical synaptic transmission long-term synaptic potentiation regulation of synaptic plasticity positive regulation of synaptic transmission regulation of trans-synaptic signaling	cell leading edge plasma membrane membrane neuron projection leading edge membrane cellular anatomical entity plasma membrane bounded cell projection neuron projection membrane cell periphery cell projection plasma membrane region cell projection membrane lamellipodium postsynapse cell leading edge plasma membrane membrane neuron projection leading edge membrane cellular anatomical entity plasma membrane bounded cell projection neuron projection membrane cell periphery cell projection plasma membrane region cell projection membrane lamellipodium postsynapse postsynaptic membrane synapse cell junction synaptic membrane myelin sheath adaxonal region myelin sheath sarcolemma basal part of cell basal plasma membrane basolateral plasma membrane intracellular anatomical structure cytoplasm glutamatergic synapse membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network neuron spine dendritic spine somatodendritic compartment dendrite dendritic tree storage vacuole vacuole perinuclear region of cytoplasm extracellular region extracellular space apical part of cell apical plasma membrane cell surface SNARE complex protein-containing complex membrane protein complex intracellular vesicle phagocytic vesicle cytoplasmic vesicle vesicle endocytic vesicle presynapse endosome Schaffer collateral - CA1 synapse secretory granule secretory vesicle specific granule lateral loop
A, B	Syntaxin-binding protein 3	protein binding binding SNARE binding syntaxin binding syntaxin-1 binding protein-containing complex binding	cellular process membrane docking protein to membrane docking developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular homeostasis cellular process membrane docking protein to membrane docking developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular homeostasis chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis intracellular chemical homeostasis intracellular glucose homeostasis trans-synaptic signaling regulation of biological process cellular localization neurotransmitter secretion transport signaling secretion biological regulation cell-cell signaling export from cell neurotransmitter transport establishment of localization cell communication chemical synaptic transmission localization signal release from synapse synaptic signaling secretion by cell signal release anterograde trans-synaptic signaling establishment of localization in cell regulation of localization hexose transmembrane transport regulation of cellular process glucose import negative regulation of biological process carbohydrate transport negative regulation of transport negative regulation of transmembrane transport negative regulation of cellular process glucose transmembrane transport regulation of glucose import regulation of transport organic substance transport transmembrane transport negative regulation of glucose import regulation of glucose transmembrane transport negative regulation of glucose transmembrane transport regulation of transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport vesicle-mediated transport organelle localization by membrane tethering exocytosis organelle localization vesicle docking exocytic process vesicle docking involved in exocytosis regulation of body fluid levels wound healing response to stimulus homotypic cell-cell adhesion cell activation hemostasis platelet aggregation blood coagulation cell adhesion cell-cell adhesion response to stress coagulation regulation of biological quality response to wounding platelet activation neutrophil activation regulated exocytosis cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity myeloid leukocyte activation leukocyte activation neutrophil mediated immunity neutrophil activation involved in immune response leukocyte activation involved in immune response neutrophil degranulation leukocyte mediated immunity immune response myeloid cell activation involved in immune response immune effector process immune system process granulocyte activation regulation of calcium ion-dependent exocytosis negative regulation of regulated secretory pathway regulation of regulated secretory pathway regulation of secretion by cell negative regulation of secretion negative regulation of exocytosis negative regulation of secretion by cell calcium-ion regulated exocytosis negative regulation of calcium ion-dependent exocytosis regulation of vesicle-mediated transport regulation of secretion regulation of exocytosis protein localization establishment of protein localization nitrogen compound transport intracellular transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport cellular response to stimulus response to organic substance biological process involved in interspecies interaction between organisms response to type II interferon response to cytokine cellular response to type II interferon response to biotic stimulus innate immune response cellular response to cytokine stimulus response to external biotic stimulus cellular response to organic substance response to other organism defense response defense response to symbiont response to external stimulus cellular response to chemical stimulus response to chemical defense response to other organism response to hormone response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to insulin response to oxygen-containing compound response to nitrogen compound hormone secretion protein localization to extracellular region peptide secretion amide transport regulation of hormone levels establishment of protein localization to extracellular region protein secretion peptide transport peptide hormone secretion hormone transport insulin secretion	cell periphery apical part of cell membrane plasma membrane plasma membrane region cellular anatomical entity apical plasma membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle cell periphery apical part of cell membrane plasma membrane plasma membrane region cellular anatomical entity apical plasma membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle vesicle endocytic vesicle basal part of cell basal plasma membrane basolateral plasma membrane endomembrane system secretory granule secretory vesicle presynapse synapse cell junction platelet alpha granule specific granule tertiary granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR000727	Target SNARE coiled-coil homology domain	Domain
C, D	IPR006012	Syntaxin/epimorphin, conserved site	Conserved Site
C, D	IPR010989	SNARE	Homologous Superfamily
C, D	IPR006011	Syntaxin, N-terminal domain	Domain
C, D	IPR045242	Syntaxin	Family
A, B	IPR043154	Sec1-like, domain 1	Homologous Superfamily
A, B	IPR036045	Sec1-like superfamily	Homologous Superfamily
A, B	IPR027482	Sec1-like, domain 2	Homologous Superfamily
A, B	IPR043127	Sec1-like, domain 3a	Homologous Superfamily
A, B	IPR001619	Sec1-like protein	Family

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.