5Z8Y

Crystal structure of human LRRTM2 in complex with Neurexin 1beta

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8038794	3000120	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8038794	3000120	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8038794	3000120	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8038794	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)
C	LRR_8_1	e5z8yC1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_1	ECOD (1.6)
E	LRR_8_1	e5z8yE1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_1	ECOD (1.6)
A	LRR_8_1	e5z8yA1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_1	ECOD (1.6)
G	LRR_8_1	e5z8yG1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_1	ECOD (1.6)
B	Laminin_G_1	e5z8yB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_1	ECOD (1.6)
D	Laminin_G_1	e5z8yD1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_1	ECOD (1.6)
H	Laminin_G_1	e5z8yH1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_1	ECOD (1.6)
F	Laminin_G_1	e5z8yF1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
E	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
A	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
G	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
B	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)
H	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
F	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, C, E, G	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat
B, D, F, H	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, C, E, G	Leucine-rich repeat transmembrane neuronal protein 2	protein binding binding signaling receptor binding neurexin family protein binding	multicellular organismal process regulation of cellular component organization regulation of cellular process regulation of postsynaptic specialization assembly cellular component organization cellular component biogenesis multicellular organism development cellular component assembly cell junction assembly regulation of excitatory synapse assembly postsynaptic density organization anatomical structure development regulation of synapse structure or activity cellular component organization or biogenesis multicellular organismal process regulation of cellular component organization regulation of cellular process regulation of postsynaptic specialization assembly cellular component organization cellular component biogenesis multicellular organism development cellular component assembly cell junction assembly regulation of excitatory synapse assembly postsynaptic density organization anatomical structure development regulation of synapse structure or activity cellular component organization or biogenesis synapse organization regulation of biological quality regulation of synapse assembly regulation of postsynaptic density organization system development developmental process regulation of biological process postsynapse organization organelle assembly postsynaptic specialization assembly postsynapse assembly biological regulation regulation of postsynapse organization nervous system development regulation of cellular component biogenesis regulation of organelle organization excitatory synapse assembly regulation of cell junction assembly regulation of synapse organization organelle organization cell junction organization regulation of organelle assembly cellular process postsynaptic specialization organization synapse assembly postsynaptic density assembly regulation of postsynaptic density assembly positive regulation of nervous system development positive regulation of cellular component organization regulation of developmental process positive regulation of biological process regulation of nervous system development positive regulation of developmental process regulation of multicellular organismal process positive regulation of cellular 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 regulation of localization import into cell receptor internalization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis regulation of receptor internalization vesicle-mediated transport localization negative regulation of cellular process regulation of endocytosis negative regulation of cellular component organization regulation of transport negative regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization endocytosis receptor-mediated endocytosis negative regulation of receptor internalization positive regulation of cell communication modulation of chemical synaptic transmission signaling cell communication long-term synaptic potentiation synaptic signaling regulation of synaptic plasticity trans-synaptic signaling regulation of signaling cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication positive regulation of signaling	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane cellular anatomical entity postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane cellular anatomical entity postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region hippocampal mossy fiber to CA3 synapse excitatory synapse Schaffer collateral - CA1 synapse extracellular region extracellular space GABA-ergic synapse glutamatergic synapse
B, D, F, H	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 fibroblast growth factor receptor binding growth factor receptor binding type 1 fibroblast growth factor receptor binding cell adhesion molecule binding 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 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	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 protein localization cellular localization gamma-aminobutyric acid receptor clustering postsynapse organization neurotransmitter-gated ion channel clustering localization within membrane protein localization to membrane localization receptor clustering cellular macromolecule localization macromolecule localization postsynaptic membrane organization behavior learning learning or memory cognition cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process 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 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 phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of protein modification process peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification 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 regulation of protein metabolic process primary metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules cell-cell adhesion via plasma-membrane adhesion molecules 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 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 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 intracellular signal transduction regulation of intracellular signal transduction positive regulation of intracellular signal transduction regulation of protein kinase A signaling protein kinase A signaling positive regulation of protein kinase A signaling 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 via plasma membrane cell adhesion molecules 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 positive regulation of ERK1 and ERK2 cascade intracellular signaling cassette positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade 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 transport regulation of signaling receptor activity regulation of AMPA receptor activity regulation of transmembrane transporter activity regulation of transporter 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 regulation of NMDA receptor activity 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 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 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 negative regulation of cellular metabolic process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process 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 organelle assembly postsynaptic specialization assembly excitatory synapse assembly gephyrin clustering involved in postsynaptic density assembly postsynaptic density assembly neuronal signal transduction regulation of catalytic activity regulation of transferase activity positive regulation of protein serine/threonine kinase activity positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity positive regulation of protein kinase C activity positive regulation of molecular function positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of protein kinase C activity	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 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 surface GABA-ergic synapse excitatory synapse endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR001611	Leucine-rich repeat	Repeat
A, C, E, G	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A, C, E, G	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
B, D, F, H	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
B, D, F, H	IPR027789	Syndecan/Neurexin domain	Domain
B, D, F, H	IPR001791	Laminin G domain	Domain
B, D, F, H	IPR003585	Neurexin/syndecan/glycophorin C	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G	Pharos: O43300	atypical teratoid rhabdoid tumor lung cancer malignant ependymoma osteosarcoma psoriasis glioblastoma lung carcinoma malignant glioma ovarian cancer invasive ductal breast carcinoma malignant colon neoplasm medulloblastoma pituitary cancer
B, D, F, H	Pharos: P58400	intellectual disability schizophrenia Pitt-Hopkins-like syndrome 2 Pitt-Hopkins syndrome Language Development Disorders autism chromosome 2P16.3 deletion syndrome autism spectrum disorder malignant colon neoplasm medulloblastoma oligodendroglioma Pick disease attention deficit hyperactivity disorder, inattentive type subependymal giant cell astrocytoma endogenous depression intellectual disability schizophrenia Pitt-Hopkins-like syndrome 2 Pitt-Hopkins syndrome Language Development Disorders autism chromosome 2P16.3 deletion syndrome autism spectrum disorder malignant colon neoplasm medulloblastoma oligodendroglioma Pick disease attention deficit hyperactivity disorder, inattentive type subependymal giant cell astrocytoma endogenous depression large cell medulloblastoma malignant ependymoma ovarian cancer Alzheimer disease pilocytic astrocytoma atypical teratoid rhabdoid tumor pituitary cancer psoriasis bipolar disorder lung carcinoma malignant glioma nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma astrocytic tumor auditory perceptual disorders primitive neuroectodermal tumor breast cancer depressive disorder glioblastoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.