3ZYM | pdb_00003zym

Structure of CALM (PICALM) in complex with VAMP8

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)
C	SCOP2 Family	SNARE fusion complex	8089357	4003812	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	SNARE fusion complex	8089358	3001549	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	GAT-like domain	8035552	3001306	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ENTH/VHS domain-like	8035555	3000164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ENTH/VHS domain-like	8035555	3000164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAT-like domain	8035552	3001306	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SNARE fusion complex	8089358	3001549	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GAT-like domain	8035552	3001306	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SNARE fusion complex	8089358	3001549	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ENTH/VHS domain-like	8035555	3000164	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)
C	WD40, eIF2A, Beta-prop_WDR5	e3zymC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: WD40, eIF2A, Beta-prop_WDR5	ECOD (v294.1)
B	WD40, eIF2A, Beta-prop_WDR5	e3zymB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: WD40, eIF2A, Beta-prop_WDR5	ECOD (v294.1)
A	Defensin_1	e3zymA2	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Immunoglobulin-related	T: Defensin-related	F: Defensin_1	ECOD (v294.1)
A	WD40, eIF2A, Beta-prop_WDR5	e3zymA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: WD40, eIF2A, Beta-prop_WDR5	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C	1.20.58.150	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	1.20.58.150	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.20.58.150	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF07651	ANTH domain (ANTH)	ANTH domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN, VESICLE-ASSOCIATED MEMBRANE PROTEIN 8	small GTPase binding protein binding binding enzyme binding GTPase binding SH3 domain binding protein domain specific binding cytoskeletal protein binding tau protein binding identical protein binding clathrin binding clathrin heavy chain binding ion binding phosphatidylinositol-4,5-bisphosphate binding small GTPase binding protein binding binding enzyme binding GTPase binding SH3 domain binding protein domain specific binding cytoskeletal protein binding tau protein binding identical protein binding clathrin binding clathrin heavy chain binding ion binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding SNARE binding 1-phosphatidylinositol binding low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor 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	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of localization regulation of biological process regulation of protein localization biological regulation intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of localization regulation of biological process regulation of protein localization biological regulation negative regulation of biological process localization negative regulation of protein localization to cell surface protein localization to cell surface macromolecule localization regulation of protein localization to cell surface intracellular protein localization negative regulation of protein localization amyloid precursor protein catabolic process regulation of cellular process positive regulation of protein metabolic process regulation of protein metabolic process positive regulation of biological process primary metabolic process regulation of amyloid precursor protein catabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process metabolic process cellular process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process positive regulation of amyloid precursor protein catabolic process amyloid precursor protein metabolic process regulation of metabolic process positive regulation of cellular process import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport regulation of cellular component organization regulation of transport regulation of vesicle-mediated transport cellular component organization cellular component organization or biogenesis regulation of endocytosis multicellular organismal process positive regulation of nervous system development axonogenesis cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process regulation of cell projection organization positive regulation of cell development nervous system development generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis regulation of nervous system development neurogenesis positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of multicellular organismal development plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization multicellular organismal-level iron ion homeostasis multicellular organismal-level homeostasis multicellular organismal-level chemical homeostasis hemopoiesis cellular localization synaptic vesicle cycle regulation of synaptic vesicle recycling presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling regulation of synaptic vesicle endocytosis establishment of localization in cell synaptic vesicle endocytosis establishment of protein localization regulation of establishment of protein localization regulation of protein transport protein transport negative regulation of transport negative regulation of endocytosis negative regulation of cellular process negative regulation of cellular component organization negative regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis vesicle localization establishment of organelle localization establishment of vesicle localization regulation of synaptic vesicle transport organelle localization synaptic vesicle localization synaptic vesicle transport membrane organization vesicle budding from membrane vesicle organization organelle organization vesicle cargo loading intracellular transport endosomal transport regulation of growth developmental growth regulation of cell morphogenesis positive regulation of developmental growth developmental growth involved in morphogenesis positive regulation of dendrite extension cell growth dendrite extension neuron projection extension regulation of developmental growth developmental cell growth growth regulation of dendrite extension positive regulation of cell growth regulation of cell growth positive regulation of growth presynapse organization regulation of terminal button organization terminal button organization regulation of synapse organization cell junction organization regulation of presynapse organization regulation of synapse structure or activity synapse organization regulation of biological quality negative regulation of protein localization to plasma membrane regulation of protein localization to membrane protein localization to cell periphery protein localization to plasma membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane negative regulation of protein localization to membrane regulation of cellular localization negative regulation of protein localization to cell periphery regulation of protein localization to plasma membrane membrane bending synaptic vesicle clustering positive regulation of transport positive regulation of synaptic vesicle clustering regulation of synaptic vesicle clustering dendrite development dendrite morphogenesis clathrin-dependent endocytosis regulation of cellular component size regulation of vesicle size regulation of anatomical structure size regulation of amyloid-beta formation positive regulation of amyloid-beta formation amyloid-beta metabolic process amyloid-beta formation clathrin coat assembly cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly behavior system process learning or memory nervous system process cognition positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription amyloid-beta clearance amyloid-beta clearance by transcytosis transcytosis negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic process synaptic vesicle maturation developmental maturation cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction regulation of Ras protein signal transduction intracellular signaling cassette signal transduction positive regulation of Ras protein signal transduction regulation of signaling Ras protein signal transduction positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling positive regulation of synaptic vesicle recycling positive regulation of endocytosis positive regulation of synaptic vesicle endocytosis cellular component disassembly catabolic process macroautophagy autophagy protein-containing complex disassembly autophagosome maturation process utilizing autophagic mechanism membrane fusion organelle membrane fusion organelle fusion 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 regulated exocytosis zymogen granule exocytosis secretion export from cell secretion by cell exocytosis calcium-ion regulated exocytosis regulation of body fluid levels secretion by tissue mucus secretion body fluid secretion regulation of pancreatic amylase secretion positive regulation of establishment of protein localization amylase secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion digestion positive regulation of protein localization digestive system process positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport regulation of secretion by cell positive regulation of secretion pancreatic juice secretion positive regulation of protein secretion pancreatic amylase secretion positive regulation of pancreatic amylase secretion negative regulation of secretion negative regulation of secretion by cell defense response to virus 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 immune response response to type II interferon response to cytokine defense response to symbiont cellular response to type II interferon response to peptide response to chemical immune system process defense response to other organism innate immune response cellular response to cytokine stimulus regulation of myeloid leukocyte mediated immunity nitrogen compound transport myeloid leukocyte activation regulation of immune system process histamine secretion by mast cell regulation of inflammatory response mast cell degranulation immune effector process histamine secretion involved in inflammatory response 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 production of molecular mediator involved in inflammatory response cell activation cell-cell signaling myeloid cell activation involved in immune response regulation of histamine secretion by mast cell exocytic process 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 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 leukocyte activation positive regulation of hormone secretion mast cell activation regulation of leukocyte degranulation mast cell mediated immunity mast cell activation involved in immune response regulation of exocytosis hormone transport	membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system endosome to plasma membrane transport vesicle intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory vesicle cytoplasm vesicle membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system endosome to plasma membrane transport vesicle intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory vesicle cytoplasm vesicle exocytic vesicle cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane clathrin-coated pit postsynaptic endocytic zone parallel fiber to Purkinje cell synapse excitatory synapse presynapse presynaptic membrane extrinsic component of plasma membrane presynaptic endocytic zone extrinsic component of presynaptic endocytic zone membrane extrinsic component of synaptic membrane presynaptic endocytic zone membrane extrinsic component of presynaptic membrane extrinsic component of membrane Golgi apparatus neurofibrillary tangle inclusion body perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body synaptic vesicle protein-containing complex plasma membrane protein complex membrane protein complex coated membrane clathrin coat membrane coat clathrin coat of coated pit clathrin-coated vesicle coated vesicle cell surface early endosome endosome postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse Schaffer collateral - CA1 synapse nucleus basal part of cell basolateral part of cell lateral part of cell cytosol basal plasma membrane basolateral plasma membrane secretory granule endosome membrane late endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane late endosome organelle membrane vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome recycling endosome zymogen granule zymogen granule membrane secretory granule membrane mitochondrion midbody azurophil granule primary lysosome azurophil granule membrane SNARE complex phagocytic vesicle endocytic vesicle mucin granule early endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR008942	ENTH/VHS	Homologous Superfamily
A, B, C	IPR011417	AP180 N-terminal homology (ANTH) domain	Domain
A, B, C	IPR045192	Clathrin coat assembly protein AP180-like	Family
A, B, C	IPR014712	ANTH domain superfamily	Homologous Superfamily
A, B, C	IPR013809	ENTH domain	Domain
A, B, C	IPR016444	Synaptobrevin/Vesicle-associated membrane protein	Family
A, B, C	IPR042855	v-SNARE, coiled-coil homology domain	Domain
A, B, C	IPR001388	Synaptobrevin-like	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.