2CJS | pdb_00002cjs

Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains as Versatile Protein-Protein Interaction Modules

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
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	d2cjsa1	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	PLC-like (P variant)	Unc-13 homolog A	RAT (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d2cjsa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	RAT (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d2cjsb2	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	PLC-like (P variant)	automated matches	RAT (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d2cjsb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	PLC-like (P variant)	8018896	4002218	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8057937	3000965	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8057937	3000965	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	HMG_CoA_synt_N	e2cjsC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: HMG_CoA_synt_N	ECOD (v294.1)
A	zf-MYND	e2cjsA1	A: a/b three-layered sandwiches	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: zf-MYND	ECOD (v294.1)
B	Alpha-L-AF_C	e2cjsB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Alpha-L-AF_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.60.120	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
A	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)
B	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF22601	RIM2-alpha zinc finger (RIM2a_ZnF)	RIM2-alpha zinc finger	This entry represents the zinc finger domain of Regulating synaptic membrane exocytosis protein 2 (RIM2a) and related proteins. This domain alone is responsible for the interaction with Munc13-1 by engaging with the Munc13-1 C2A domain [1]. Structura ...	This entry represents the zinc finger domain of Regulating synaptic membrane exocytosis protein 2 (RIM2a) and related proteins. This domain alone is responsible for the interaction with Munc13-1 by engaging with the Munc13-1 C2A domain [1]. Structurally, this domain is similar to FIVE zinc fingers.	Domain
A, B	PF00168	C2 domain (C2)	C2 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	REGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 2	small GTPase binding protein binding binding enzyme binding GTPase binding protein domain specific binding protein-macromolecule adaptor activity molecular adaptor activity transmembrane transporter binding protein-containing complex binding structural constituent of presynaptic active zone structural molecule activity structural constituent of synapse cation binding small GTPase binding protein binding binding enzyme binding GTPase binding protein domain specific binding protein-macromolecule adaptor activity molecular adaptor activity transmembrane transporter binding protein-containing complex binding structural constituent of presynaptic active zone structural molecule activity structural constituent of synapse cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular localization regulated exocytosis transport signaling synaptic vesicle cycle synaptic vesicle exocytosis membrane docking vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization organelle localization by membrane tethering synaptic signaling secretion by cell organelle localization cellular localization regulated exocytosis transport signaling synaptic vesicle cycle synaptic vesicle exocytosis membrane docking vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization organelle localization by membrane tethering synaptic signaling secretion by cell organelle localization signal release establishment of localization in cell vesicle docking involved in exocytosis trans-synaptic signaling regulation of biological process neurotransmitter secretion secretion biological regulation export from cell cell-cell signaling neurotransmitter transport synaptic vesicle docking establishment of localization chemical synaptic transmission signal release from synapse exocytosis anterograde trans-synaptic signaling vesicle docking exocytic process cellular process cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic positive regulation of response to stimulus modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway nervous system process regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus regulation of cell communication excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling developmental process cellular developmental process cell differentiation positive regulation of inhibitory postsynaptic potential positive regulation of nervous system process modulation of inhibitory postsynaptic potential inhibitory postsynaptic potential positive regulation of multicellular organismal process calcium-ion regulated exocytosis regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway spontaneous synaptic transmission spontaneous neurotransmitter secretion establishment of protein localization intracellular transport protein transport macromolecule localization intracellular protein localization intracellular protein transport calcium ion-regulated exocytosis of neurotransmitter positive regulation of organelle organization regulation of localization membrane fusion vesicle organization regulation of calcium-dependent activation of synaptic vesicle fusion positive regulation of synaptic vesicle fusion to presynaptic active zone membrane regulation of synaptic vesicle membrane organization endomembrane system organization vesicle fusion to plasma membrane positive regulation of synaptic vesicle membrane organization regulation of organelle organization organelle fusion positive regulation of vesicle fusion vesicle fusion regulation of cellular component organization positive regulation of cellular component organization organelle membrane fusion calcium-dependent activation of synaptic vesicle fusion regulation of vesicle fusion cellular component organization cellular component organization or biogenesis membrane organization regulation of synaptic vesicle fusion to presynaptic active zone membrane regulation of transport synaptic vesicle fusion to presynaptic active zone membrane regulation of vesicle-mediated transport organelle organization positive regulation of transport synaptic vesicle membrane organization regulation of secretion regulation of secretion by cell regulation of exocytosis synaptic vesicle priming cellular component biogenesis cellular component assembly protein-containing complex assembly protein-containing complex organization regulation of regulated secretory pathway regulation of neurotransmitter transport regulation of synaptic vesicle exocytosis regulation of neurotransmitter secretion nitrogen compound transport hormone secretion protein localization to extracellular region peptide secretion regulation of hormone levels establishment of protein localization to extracellular region protein secretion peptide transport peptide hormone secretion hormone transport insulin secretion regulation of growth developmental growth cell projection organization neuron projection development regulation of cell morphogenesis positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis anatomical structure development positive regulation of developmental growth system development nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of dendrite extension regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis neurogenesis dendrite extension regulation of anatomical structure morphogenesis neuron projection extension regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth regulation of dendrite extension positive regulation of cell growth regulation of cell growth anatomical structure morphogenesis positive regulation of growth neuron development	cell periphery presynapse cellular anatomical structure synapse cell junction membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane cell cortex intracellular anatomical structure cytoplasmic region presynaptic active zone cytoplasmic component cell periphery presynapse cellular anatomical structure synapse cell junction membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane cell cortex intracellular anatomical structure cytoplasmic region presynaptic active zone cytoplasmic component cell cortex region cytoplasm presynaptic active zone protein-containing complex GABA-ergic synapse glutamatergic synapse photoreceptor ribbon synapse ribbon synapse inhibitory synapse
A, B	UNC-13 HOMOLOG A	protein binding binding SNARE binding syntaxin binding lipid binding diacylglycerol binding phospholipid binding protein-containing complex binding calmodulin binding identical protein binding cytoskeletal protein binding spectrin binding cation binding ion binding protein binding binding SNARE binding syntaxin binding lipid binding diacylglycerol binding phospholipid binding protein-containing complex binding calmodulin binding identical protein binding cytoskeletal protein binding spectrin binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein domain specific binding syntaxin-1 binding transition metal ion binding zinc ion binding	vesicle localization establishment of organelle localization cellular localization regulated exocytosis transport secretion establishment of vesicle localization neuronal dense core vesicle exocytosis export from cell dense core granule exocytosis establishment of localization vesicle-mediated transport localization dense core granule localization secretion by cell vesicle localization establishment of organelle localization cellular localization regulated exocytosis transport secretion establishment of vesicle localization neuronal dense core vesicle exocytosis export from cell dense core granule exocytosis establishment of localization vesicle-mediated transport localization dense core granule localization secretion by cell exocytosis organelle localization establishment of localization in cell secretory granule localization cellular process calcium-ion regulated exocytosis membrane organization protein-containing complex organization membrane fusion organelle membrane fusion cellular component organization cellular component biogenesis vesicle organization organelle fusion organelle organization cellular component assembly protein-containing complex assembly SNARE complex assembly cellular component organization or biogenesis vesicle fusion regulation of biological process amyloid precursor protein catabolic process regulation of cellular process regulation of protein metabolic process biological regulation regulation of amyloid precursor protein catabolic process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process metabolic process protein metabolic process macromolecule metabolic process amyloid precursor protein metabolic process regulation of metabolic process regulation of synaptic plasticity trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication positive regulation of synaptic plasticity synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of biological quality positive regulation of organelle organization regulation of localization regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process regulation of vesicle fusion positive regulation of cellular process regulation of transport regulation of vesicle-mediated transport regulation of organelle organization positive regulation of transport positive regulation of vesicle fusion synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse regulation of calcium-dependent activation of synaptic vesicle fusion positive regulation of synaptic vesicle fusion to presynaptic active zone membrane regulation of synaptic vesicle membrane organization endomembrane system organization vesicle fusion to plasma membrane neurotransmitter secretion neurotransmitter transport positive regulation of synaptic vesicle membrane organization signal release from synapse calcium-dependent activation of synaptic vesicle fusion signal release regulation of synaptic vesicle fusion to presynaptic active zone membrane synaptic vesicle fusion to presynaptic active zone membrane synaptic vesicle membrane organization exocytic process synaptic vesicle priming regulation of synaptic vesicle priming regulation of protein-containing complex assembly regulation of cellular component biogenesis multicellular organismal process regulation of growth developmental growth cell projection organization neuron projection development regulation of cell morphogenesis positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of developmental growth system development developmental process nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of dendrite extension cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis neurogenesis dendrite extension regulation of anatomical structure morphogenesis neuron projection extension regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth regulation of dendrite extension positive regulation of cell growth regulation of cell growth anatomical structure morphogenesis positive regulation of growth neuron development amyloid-beta metabolic process membrane docking organelle localization by membrane tethering vesicle docking involved in exocytosis synaptic vesicle docking vesicle docking dense core granule priming cell junction organization neuromuscular junction development synapse organization regulation of neuronal synaptic plasticity regulation of short-term neuronal synaptic plasticity positive regulation of cell communication cellular response to stimulus positive regulation of signal transduction response to stimulus regulation of signal transduction glutamate receptor signaling pathway positive regulation of response to stimulus positive regulation of glutamate receptor signaling pathway signal transduction cell surface receptor signaling pathway regulation of glutamate receptor signaling pathway regulation of response to stimulus positive regulation of signaling positive regulation of neurotransmitter secretion positive regulation of secretion by cell regulation of secretion by cell positive regulation of secretion positive regulation of neurotransmitter transport regulation of neurotransmitter transport positive regulation of synaptic transmission regulation of secretion regulation of neurotransmitter secretion nerve development innervation long-term synaptic potentiation synaptic transmission, glutamatergic synaptic vesicle maturation developmental maturation	presynapse cellular anatomical structure synapse cell junction presynaptic active zone cell periphery membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane glutamatergic synapse neuromuscular junction axon presynapse cellular anatomical structure synapse cell junction presynaptic active zone cell periphery membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane glutamatergic synapse neuromuscular junction axon neuron projection axon terminus plasma membrane bounded cell projection cell projection distal axon calyx of Held neuron projection terminus membrane-bounded organelle intracellular anatomical structure intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane vesicle transport vesicle exocytic vesicle membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane organelle secretory vesicle cytoplasm organelle membrane exocytic vesicle terminal bouton Golgi-associated vesicle protein-containing complex excitatory synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR054386	RIM, zinc finger	Domain
C	IPR017455	Zinc finger, FYVE-related	Domain
C	IPR000008	C2 domain	Domain
C	IPR010911	Rab-binding domain	Domain
C	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C	IPR036034	PDZ superfamily	Homologous Superfamily
C	IPR039032	Rim-like	Family
C	IPR035892	C2 domain superfamily	Homologous Superfamily
C	IPR001478	PDZ domain	Domain
A, B	IPR014770	Munc13 homology 1	Domain
A, B	IPR037302	Protein Unc-13, C2B domain	Domain
A, B	IPR014772	Mammalian uncoordinated homology 13, domain 2	Domain
A, B	IPR027080	Protein Unc-13	Family
A, B	IPR000008	C2 domain	Domain
A, B	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
A, B	IPR035892	C2 domain superfamily	Homologous Superfamily
A, B	IPR010439	MUN domain	Domain
A, B	IPR046349	C1-like domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Monotopic/peripheral	All beta monotopic/peripheral	C2 domain	C2 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.