3VKF | pdb_00003vkf

Crystal Structure of Neurexin 1beta/Neuroligin 1 complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Rrf2	e3vkfD1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: Rrf2	ECOD (develop294)
C	HATPase_c	e3vkfC1	A: alpha bundles	X: Flavodoxin-like	H: SH3	T: SH3	F: HATPase_c	ECOD (develop294)
B	SIS	e3vkfB1	A: alpha bundles	X: Ribosomal protein L31e-like	H: Reductive activator for corrinoid/iron-sulfur protein second domain	T: Reductive activator for corrinoid/iron-sulfur protein second domain	F: SIS	ECOD (develop294)
A	HATPase_c	e3vkfA1	A: alpha bundles	X: Flavodoxin-like	H: SH3	T: SH3	F: HATPase_c	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
A	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF02210	Laminin G domain (Laminin_G_2)	Laminin G domain	This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Neurexin-1-beta	cation binding ion binding binding metal ion binding small molecule binding	developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development cell adhesion cellular process	cell periphery cellular anatomical structure plasma membrane membrane presynapse synapse cell junction presynaptic membrane plasma membrane region synaptic membrane
A, B	Neuroligin-1	cell adhesion molecule binding protein binding binding cell adhesion mediator activity protein-containing complex binding signaling receptor binding neurexin family protein binding identical protein binding molecular transducer activity signaling receptor activity PDZ domain binding protein domain specific binding scaffold protein binding	developmental process multicellular organismal process nervous system development developmental maturation synapse maturation cellular component organization cell-cell adhesion involved in synapse maturation multicellular organism development cell adhesion cell junction organization cell-cell adhesion anatomical structure development cellular process synapse organization developmental process multicellular organismal process nervous system development developmental maturation synapse maturation cellular component organization cell-cell adhesion involved in synapse maturation multicellular organism development cell adhesion cell junction organization cell-cell adhesion anatomical structure development cellular process synapse organization cellular component organization or biogenesis system development cellular response to stimulus positive regulation of cell communication regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling 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 cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling membrane organization cellular localization postsynapse organization AMPA glutamate receptor clustering glutamate receptor clustering neurotransmitter-gated ion channel clustering localization within membrane protein localization to membrane localization receptor clustering macromolecule localization intracellular protein localization postsynaptic membrane organization vesicle localization establishment of organelle localization transport establishment of vesicle localization establishment of localization organelle localization establishment of localization in cell synaptic vesicle localization synaptic vesicle transport membrane biogenesis presynaptic membrane assembly cellular component biogenesis presynaptic membrane organization cellular component assembly cell junction assembly presynapse organization membrane assembly neurexin clustering involved in presynaptic membrane assembly synapse assembly presynapse assembly heterophilic cell-cell adhesion organelle organization postsynaptic density protein 95 clustering postsynaptic density organization postsynaptic specialization organization regulation of developmental process cellular developmental process cell projection organization positive regulation of dendritic spine development cell development regulation of dendritic spine development neuron projection development positive regulation of developmental process neurogenesis neuron differentiation dendrite development cell differentiation dendritic spine development plasma membrane bounded cell projection organization generation of neurons neuron development maintenance of synapse structure cell junction maintenance cellular component maintenance cellular response to metal ion cellular response to chemical stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion positive regulation of neuromuscular synaptic transmission regulation of neuromuscular synaptic transmission positive regulation of synaptic transmission neuromuscular synaptic transmission regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization positive regulation of neuron projection development positive regulation of cell projection organization regulation of cell projection organization regulation of plasma membrane bounded cell projection organization neuron cell-cell adhesion regulation of postsynaptic specialization assembly regulation of excitatory synapse assembly regulation of synapse structure or activity regulation of synapse assembly regulation of postsynaptic density organization organelle assembly postsynaptic specialization assembly postsynapse assembly regulation of postsynapse organization regulation of cellular component biogenesis regulation of organelle organization excitatory synapse assembly regulation of cell junction assembly regulation of synapse organization regulation of organelle assembly postsynaptic density assembly regulation of postsynaptic density assembly positive regulation of intracellular signal transduction intracellular signal transduction regulation of intracellular signal transduction establishment of protein localization protein targeting regulation of localization regulated exocytosis positive regulation of neurotransmitter secretion synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport vesicle-mediated transport in synapse positive regulation of regulated secretory pathway positive regulation of neurotransmitter transport neurotransmitter secretion regulation of synaptic vesicle exocytosis neurotransmitter transport regulation of secretion signal release from synapse exocytosis positive regulation of secretion by cell positive regulation of exocytosis regulation of regulated secretory pathway regulation of secretion by cell secretion by cell positive regulation of secretion signal release positive regulation of synaptic vesicle exocytosis regulation of transport secretion regulation of neurotransmitter transport export from cell regulation of vesicle-mediated transport positive regulation of transport regulation of neurotransmitter secretion regulation of exocytosis cortical cytoskeleton organization cytoskeleton organization cytoskeletal matrix organization at active zone ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway NMDA selective glutamate receptor signaling pathway NMDA glutamate receptor clustering presynaptic active zone organization positive regulation of presynaptic active zone assembly regulation of presynapse assembly regulation of presynaptic active zone assembly regulation of presynapse organization positive regulation of presynapse assembly presynaptic active zone assembly calcium-dependent cell-cell adhesion ruffle organization plasma membrane bounded cell projection assembly ruffle assembly positive regulation of cellular component biogenesis regulation of cell projection assembly positive regulation of ruffle assembly regulation of plasma membrane bounded cell projection assembly regulation of ruffle assembly cell projection assembly positive regulation of plasma membrane bounded cell projection assembly terminal button organization protein localization to synapse regulation of protein localization positive regulation of protein localization to synapse regulation of protein localization to synapse positive regulation of protein localization protein localization to cell junction positive regulation of nervous system development regulation of nervous system development regulation of multicellular organismal development positive regulation of cell junction assembly positive regulation of multicellular organismal process positive regulation of synapse assembly synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission, glutamatergic regulation of signaling receptor activity regulation of transmembrane transporter activity regulation of NMDA receptor activity transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of neurotransmitter receptor activity synaptic membrane adhesion positive regulation of synaptic transmission, GABAergic synaptic transmission, GABAergic regulation of synaptic transmission, GABAergic respiratory gaseous exchange by respiratory system respiratory system process regulation of respiratory gaseous exchange regulation of respiratory system process regulation of respiratory gaseous exchange by nervous system process receptor localization to synapse synaptic vesicle clustering positive regulation of synaptic vesicle clustering regulation of synaptic vesicle clustering plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis anatomical structure morphogenesis neuronal ion channel clustering anatomical structure maturation neuron maturation cell maturation negative regulation of biological process negative regulation of dendritic spine morphogenesis dendritic spine morphogenesis dendritic spine organization negative regulation of cellular component organization negative regulation of dendritic spine development negative regulation of cellular process negative regulation of cell projection organization regulation of anatomical structure morphogenesis negative regulation of developmental process dendrite morphogenesis cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development regulation of dendritic spine morphogenesis neuron projection organization regulation of cell differentiation regulation of neuron differentiation rhythmic process AMPA selective glutamate receptor signaling pathway filopodium assembly regulation of filopodium assembly positive regulation of filopodium assembly postsynaptic membrane assembly neuron projection arborization circadian sleep/wake cycle rhythmic behavior circadian rhythm regulation of circadian sleep/wake cycle regulation of circadian sleep/wake cycle, wakefulness regulation of circadian rhythm behavior regulation of behavior circadian behavior positive regulation of behavior positive regulation of circadian rhythm circadian sleep/wake cycle, wakefulness positive regulation of circadian sleep/wake cycle, wakefulness circadian sleep/wake cycle process synaptic vesicle targeting vesicle targeting exocytic process long-term synaptic potentiation regulation of synaptic plasticity import into cell positive regulation of synaptic vesicle recycling regulation of synaptic vesicle recycling presynaptic endocytosis synaptic vesicle recycling positive regulation of endocytosis regulation of synaptic vesicle endocytosis positive regulation of synaptic vesicle endocytosis regulation of endocytosis synaptic vesicle endocytosis endocytosis	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein complex involved in cell-cell adhesion protein-containing complex protein complex involved in cell adhesion synaptic cleft extracellular region somatodendritic compartment cell projection cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein complex involved in cell-cell adhesion protein-containing complex protein complex involved in cell adhesion synaptic cleft extracellular region somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection synapse cell junction glutamatergic synapse receptor complex neuromuscular junction membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system dendritic shaft neuron spine dendritic spine postsynapse neuron to neuron synapse inhibitory synapse filopodium tip actin-based cell projection filopodium postsynaptic specialization membrane postsynaptic specialization synaptic membrane postsynaptic membrane plasma membrane region presynapse GABA-ergic synapse excitatory synapse postsynaptic density asymmetric synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
C, D	IPR001791	Laminin G domain	Domain
C, D	IPR050372	Neurexin-related cell adhesion and synaptic protein	Family
C, D	IPR027789	Syndecan/Neurexin domain	Domain
C, D	IPR003585	Neurexin/syndecan/glycophorin C	Domain
A, B	IPR051093	Neuroligin and Bile salt-activated lipase	Family
A, B	IPR002018	Carboxylesterase, type B	Domain
A, B	IPR019819	Carboxylesterase type B, conserved site	Conserved Site
A, B	IPR000460	Neuroligin	Family
A, B	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily

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.