2XB6

Revisited crystal structure of Neurexin1beta-Neuroligin4 complex

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
Pharos: Disease Associations
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	d2xb6a1	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2xb6a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2xb6b1	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2xb6b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2xb6c_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Laminin G-like module	automated matches	RAT (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d2xb6d_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Laminin G-like module	automated matches	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)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8036535	3000120	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8036535	3000120	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	PF00135	e2xb6A1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: PF00135	ECOD (1.6)
B	PF00135	e2xb6B1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: PF00135	ECOD (1.6)
C	PF02210	e2xb6C1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF02210	ECOD (1.6)
D	PF02210	e2xb6D1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF02210	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00135	Carboxylesterase family (COesterase)	Carboxylesterase family	-	Domain
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
A, B	NEUROLIGIN-4, X-LINKED	molecular transducer activity signaling receptor activity cell adhesion molecule binding protein binding binding scaffold protein binding ion binding anion binding chloride ion binding small molecule binding identical protein binding protein homodimerization activity protein dimerization activity signaling receptor binding molecular transducer activity signaling receptor activity cell adhesion molecule binding protein binding binding scaffold protein binding ion binding anion binding chloride ion binding small molecule binding identical protein binding protein homodimerization activity protein dimerization activity signaling receptor binding neurexin family protein binding	synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell cellular process endocytosis synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell cellular process endocytosis developmental process anatomical structure development brainstem development behavior multicellular organismal process system process learning learning or memory nervous system process cognition developmental growth growth organ growth membrane organization presynapse organization nervous system development membrane biogenesis presynaptic membrane assembly membrane assembly cellular component organization cellular component biogenesis presynaptic membrane organization multicellular organism development cellular component assembly cell junction organization cell junction assembly cellular component organization or biogenesis synapse organization synapse assembly presynapse assembly system development adult behavior cellular developmental process generation of neurons neurogenesis neuron differentiation cell differentiation head development animal organ development brain development cerebellum development central nervous system development metencephalon development hindbrain development trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication cell adhesion cell-cell adhesion neuron cell-cell adhesion biological process involved in intraspecies interaction between organisms social behavior cellular response to stimulus regulation of postsynaptic membrane potential response to stimulus regulation of system process negative regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality cell surface receptor signaling pathway regulation of nervous system process regulation of response to stimulus negative regulation of excitatory postsynaptic potential excitatory postsynaptic potential regulation of membrane potential postsynapse organization postsynaptic membrane assembly postsynapse assembly postsynaptic membrane organization vocalization behavior cell-cell junction organization	neuron to neuron synapse synapse cell junction asymmetric synapse glutamatergic synapse cellular anatomical entity excitatory synapse asymmetric, glutamatergic, excitatory synapse postsynaptic specialization membrane postsynaptic specialization membrane plasma membrane postsynaptic density membrane synaptic membrane neuron to neuron synapse synapse cell junction asymmetric synapse glutamatergic synapse cellular anatomical entity excitatory synapse asymmetric, glutamatergic, excitatory synapse postsynaptic specialization membrane postsynaptic specialization membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse organelle postsynaptic membrane plasma membrane region cell surface presynapse somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection symmetric synapse GABA-ergic synapse symmetric, GABA-ergic, inhibitory synapse inhibitory synapse
C, D	NEUREXIN-1-BETA	protein-containing complex binding binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity cation binding ion binding calcium ion binding metal ion binding small molecule binding protein binding signaling receptor binding fibroblast growth factor receptor binding growth factor receptor binding protein-containing complex binding binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity cation binding ion binding calcium ion binding metal ion binding small molecule binding protein binding signaling receptor binding fibroblast growth factor receptor binding growth factor receptor binding type 1 fibroblast growth factor receptor binding cell adhesion molecule binding neuroligin family protein binding calcium-dependent protein binding channel regulator activity ion channel regulator activity calcium channel regulator activity molecular function regulator activity transporter regulator activity acetylcholine receptor binding	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 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 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 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 cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling membrane organization protein localization cellular localization gamma-aminobutyric acid receptor clustering postsynapse organization neurotransmitter-gated ion channel clustering localization within membrane protein localization to membrane cellular component organization localization cell junction organization receptor clustering cellular macromolecule localization macromolecule localization cellular component organization or biogenesis synapse organization postsynaptic membrane organization learning or memory learning imitative learning auditory behavior vocal learning learned vocalization behavior or vocal learning response to mechanical stimulus cognition response to external stimulus mechanosensory behavior behavior response to auditory stimulus observational learning response to abiotic stimulus positive regulation of protein localization to plasma membrane regulation of localization regulation of protein localization regulation of protein localization to membrane positive regulation of protein localization to cell periphery protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to membrane regulation of protein localization to cell periphery regulation of cellular localization positive regulation of protein localization regulation of protein localization to plasma membrane positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-serine phosphorylation positive regulation of cellular metabolic process positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process organic substance metabolic process peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification regulation of phosphorus metabolic process metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules cell adhesion cell-cell adhesion cell-cell adhesion via plasma-membrane adhesion molecules organelle organization postsynaptic density protein 95 clustering postsynaptic density organization postsynaptic specialization organization cellular response to inorganic substance cellular response to metal ion response to inorganic substance 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 response to fibroblast growth factor cellular response to growth factor stimulus positive regulation of fibroblast growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus fibroblast growth factor receptor signaling pathway response to growth factor cellular response to fibroblast growth factor stimulus regulation of fibroblast growth factor receptor signaling pathway regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process cell projection organization cell development neuron projection development neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization neuron cell-cell adhesion regulation of postsynaptic specialization assembly cellular component biogenesis cellular component assembly cell junction 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 synapse assembly postsynaptic density assembly regulation of postsynaptic density assembly 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 presynapse organization presynaptic active zone assembly presynapse assembly guanylate kinase-associated protein clustering rhythmic process circadian rhythm positive regulation of nervous system development regulation of developmental process regulation of nervous system development positive regulation of developmental process regulation of multicellular organismal development positive regulation of cellular component biogenesis positive regulation of cell junction assembly positive regulation of multicellular organismal process positive regulation of synapse assembly establishment of protein localization establishment of localization intracellular signal transduction positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission, glutamatergic membrane biogenesis presynaptic membrane assembly membrane assembly presynaptic membrane organization transport regulation of signaling receptor activity regulation of transmembrane transporter activity regulation of transporter activity regulation of NMDA receptor activity regulation of monoatomic ion transmembrane transporter activity regulation of transport 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 adult behavior protein localization to synapse protein localization to cell junction receptor localization to synapse protein-containing complex localization neuromuscular process neuromuscular process controlling balance vesicle localization synaptic vesicle clustering synaptic vesicle cycle vesicle-mediated transport vesicle-mediated transport in synapse organelle localization establishment of localization in cell synaptic vesicle localization biological process involved in intraspecies interaction between organisms social behavior cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process organic substance biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process developmental maturation synapse maturation cell-cell adhesion involved in synapse maturation regulation of synapse maturation positive regulation of synapse maturation positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of gene expression positive regulation of cellular biosynthetic process postsynaptic membrane assembly neuroligin clustering involved in postsynaptic membrane assembly regulation of behavior regulation of grooming behavior grooming behavior maintenance of synapse structure cell junction maintenance cellular component maintenance filopodium assembly negative regulation of filopodium assembly regulation of filopodium assembly plasma membrane bounded cell projection assembly negative regulation of plasma membrane bounded cell projection assembly negative regulation of cell projection organization negative regulation of cellular component organization regulation of cell projection assembly regulation of plasma membrane bounded cell projection assembly cell projection assembly startle response regulation of response to external stimulus negative regulation of response to stimulus prepulse inhibition negative regulation of response to external stimulus regulation of protein kinase A signaling protein kinase A signaling positive regulation of protein kinase A signaling protein-containing complex organization protein-containing complex assembly involved in synapse maturation protein-containing complex assembly calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules regulation of synaptic vesicle cycle regulation of vesicle-mediated transport blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development neurotransmitter secretion secretion export from cell neurotransmitter transport signal release from synapse secretion by cell signal release regulation of AMPA receptor activity anatomical structure maturation neuron maturation cell maturation trans-synaptic signaling, modulating synaptic transmission trans-synaptic signaling by endocannabinoid regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission trans-synaptic signaling by lipid, modulating synaptic transmission trans-synaptic signaling by lipid trans-synaptic signaling by endocannabinoid, modulating synaptic transmission regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis vocalization behavior cerebellar cortex morphogenesis hindbrain morphogenesis central nervous system neuron differentiation cerebellar granular layer morphogenesis metencephalon development cerebellar cortex formation cerebellum morphogenesis head development animal organ development brain development cerebellar granular layer development glutamatergic neuron differentiation cerebellar cortex development cerebellum development central nervous system development cerebellar granule cell differentiation hindbrain development cerebellar granular layer formation cell differentiation in hindbrain gephyrin clustering involved in postsynaptic density assembly	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane protein complex involved in cell-cell adhesion membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane protein complex involved in cell-cell adhesion protein-containing complex protein complex involved in cell adhesion neuromuscular junction synapse cell junction inhibitory synapse growth cone axon cell projection distal axon neuron projection axonal growth cone plasma membrane bounded cell projection site of polarized growth cell surface cell periphery plasma membrane GABA-ergic synapse presynaptic active zone membrane presynaptic membrane synaptic membrane presynapse plasma membrane region presynaptic active zone excitatory synapse Schaffer collateral - CA1 synapse intracellular vesicle cytoplasmic vesicle cytoplasm vesicle endocytic vesicle glutamatergic synapse somatodendritic compartment cell body neuronal cell body neuron to neuron synapse endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
C, D	IPR001791	Laminin G domain	Domain
C, D	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
C, D	IPR027789	Syndecan/Neurexin domain	Domain
C, D	IPR003585	Neurexin/syndecan/glycophorin C	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8N0W4	Asperger syndrome, X-linked, susceptibility to, 2 autism autism, susceptibility to, X-linked 2 pancreatic intraductal papillary-mucinous neoplasm Alcoholic Intoxication, Chronic autism spectrum disorder colorectal cancer malignant colon neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Asperger syndrome atypical teratoid rhabdoid tumor breast cancer intellectual disability malignant ependymoma Asperger syndrome, X-linked, susceptibility to, 2 autism autism, susceptibility to, X-linked 2 pancreatic intraductal papillary-mucinous neoplasm Alcoholic Intoxication, Chronic autism spectrum disorder colorectal cancer malignant colon neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Asperger syndrome atypical teratoid rhabdoid tumor breast cancer intellectual disability malignant ependymoma pancreatic intraductal papillary-mucinous carcinoma chronic kidney disease large cell medulloblastoma medulloblastoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Monotopic/peripheral	Alpha/Beta monotopic/peripheral	Alpha/beta-hydrolases	Acetylcholinesterase-like

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 R01GM133198.