2XB6 | pdb_00002xb6

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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8036535	3000120	SCOP2B (2022-06-29)
C	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)
D		e2xb6D1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
C		e2xb6C1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
B		e2xb6B1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
A		e2xb6A1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)

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
A, B	PF00135	Carboxylesterase family (COesterase)	Carboxylesterase family		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 molecular transducer activity transmembrane signaling receptor activity signaling receptor activity protein binding signaling receptor binding cell adhesion molecule binding neuroligin family protein binding calcium-dependent 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 gamma-aminobutyric acid receptor clustering postsynapse organization neurotransmitter-gated ion channel clustering localization within membrane protein localization to membrane localization receptor clustering macromolecule localization intracellular protein localization postsynaptic membrane organization 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 postsynaptic membrane assembly membrane biogenesis cellular component biogenesis cellular component assembly cell junction assembly postsynapse assembly neuroligin clustering involved in postsynaptic membrane assembly membrane assembly synapse assembly heterophilic cell-cell adhesion organelle organization postsynaptic density protein 95 clustering postsynaptic density organization postsynaptic specialization organization 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 cellular developmental process cell projection organization cell development neuron projection development neurogenesis neuron differentiation positive regulation of neuron projection development cell differentiation positive regulation of cell projection organization plasma membrane bounded cell projection organization regulation of cell projection organization generation of neurons neuron development regulation of plasma membrane bounded cell projection organization filopodium assembly negative regulation of filopodium assembly negative regulation of biological process regulation of filopodium assembly plasma membrane bounded cell projection assembly negative regulation of plasma membrane bounded cell projection assembly negative regulation of cellular process negative regulation of cell projection organization negative regulation of cellular component organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly cell projection assembly neuron cell-cell adhesion 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 protein-containing complex organization protein-containing complex assembly involved in synapse maturation protein-containing complex assembly 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 regulation of synapse structure or activity regulation of synapse assembly positive regulation of presynapse assembly presynapse organization regulation of cell junction assembly regulation of synapse organization presynaptic active zone assembly presynapse assembly guanylate kinase-associated protein clustering calcium-dependent cell-cell adhesion 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 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 synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission, glutamatergic presynaptic membrane assembly presynaptic membrane organization positive regulation of synaptic transmission, GABAergic synaptic transmission, GABAergic regulation of synaptic transmission, GABAergic protein localization to synapse protein localization to cell junction receptor localization to synapse plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis vesicle localization transport synaptic vesicle clustering synaptic vesicle cycle vesicle-mediated transport vesicle-mediated transport in synapse organelle localization establishment of localization in cell synaptic vesicle localization AMPA selective glutamate receptor signaling pathway 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 organelle assembly postsynaptic specialization assembly excitatory synapse assembly gephyrin clustering involved in postsynaptic density assembly postsynaptic density assembly	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane protein complex involved in cell-cell adhesion membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane protein complex involved in cell-cell adhesion protein-containing complex protein complex involved in cell adhesion cell periphery presynapse synapse cell junction plasma membrane presynaptic membrane plasma membrane region synaptic membrane intracellular vesicle cytoplasmic vesicle cytoplasm vesicle endocytic vesicle glutamatergic synapse neuromuscular junction somatodendritic compartment cell body neuronal cell body neuron to neuron synapse inhibitory synapse growth cone axon cell projection distal axon neuron projection axonal growth cone plasma membrane bounded cell projection site of polarized growth cell-cell junction anchoring junction filtration diaphragm slit diaphragm cell surface GABA-ergic synapse excitatory synapse endoplasmic reticulum
A, B	NEUROLIGIN-4, X-LINKED	cell adhesion molecule binding protein binding binding scaffold protein binding cell adhesion mediator activity 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	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 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 process 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 regulation of cellular component organization regulation of synapse structure or activity regulation of synapse assembly regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization vocalization behavior cell-cell junction organization	cellular anatomical structure neuron to neuron synapse synapse cell junction asymmetric synapse glutamatergic synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse postsynaptic specialization membrane postsynaptic specialization membrane plasma membrane postsynaptic density membrane synaptic membrane cellular anatomical structure neuron to neuron synapse synapse cell junction asymmetric synapse glutamatergic synapse 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 somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection GABA-ergic synapse symmetric synapse symmetric, GABA-ergic, inhibitory synapse inhibitory synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR050372	Neurexin-related cell adhesion and synaptic protein	Family
C, D	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
C, D	IPR027789	Syndecan/Neurexin domain	Domain
C, D	IPR001791	Laminin G domain	Domain
C, D	IPR003585	Neurexin/syndecan/glycophorin C	Domain
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
A, B	IPR051093	Neuroligin and Bile salt-activated lipase	Family

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.