5KCA

Crystal structure of the Cbln1 C1q domain trimer in complex with the amino-terminal domain (ATD) of iGluR Delta-2 (GluD2)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	SCOP2B Superfamily	TNF-like	8070850	3000061	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	PF00386	e5kcaA3	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: PF00386	ECOD (1.6)
A	PF01094	e5kcaA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF01094	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01094	Receptor family ligand binding region (ANF_receptor)	Receptor family ligand binding region	-	Family
A	PF00386	C1q domain (C1q)	C1q domain	C1q is a subunit of the C1 enzyme complex that activates the serum complement system.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Cerebellin-1,Cerebellin-1,Cerebellin-1,Glutamate receptor ionotropic, delta-2	identical protein binding protein binding binding PDZ domain binding protein domain specific binding glutamate receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity scaffold protein binding transmitter-gated monoatomic ion channel activity gated channel activity monoatomic ion channel activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential identical protein binding protein binding binding PDZ domain binding protein domain specific binding glutamate receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity scaffold protein binding transmitter-gated monoatomic ion channel activity gated channel activity monoatomic ion channel activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential neurotransmitter receptor activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity postsynaptic neurotransmitter receptor activity passive transmembrane transporter activity neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential channel activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	multicellular organismal process regulation of cellular component organization regulation of cellular process regulation of developmental process negative regulation of biological process cellular component organization cellular component biogenesis regulation of nervous system development multicellular organism development cellular component assembly negative regulation of cell junction assembly cell junction assembly anatomical structure development negative regulation of cellular process multicellular organismal process regulation of cellular component organization regulation of cellular process regulation of developmental process negative regulation of biological process cellular component organization cellular component biogenesis regulation of nervous system development multicellular organism development cellular component assembly negative regulation of cell junction assembly cell junction assembly anatomical structure development negative regulation of cellular process regulation of synapse structure or activity negative regulation of nervous system development regulation of multicellular organismal process synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality system development developmental process regulation of biological process regulation of multicellular organismal development inhibitory synapse assembly negative regulation of cellular component organization negative regulation of developmental process biological regulation nervous system development negative regulation of synapse organization regulation of cellular component biogenesis negative regulation of inhibitory synapse assembly regulation of cell junction assembly regulation of synapse organization cell junction organization cellular process synapse assembly negative regulation of multicellular organismal process negative regulation of synapse assembly regulation of inhibitory synapse assembly regulation of postsynaptic specialization assembly regulation of excitatory synapse assembly postsynaptic density organization regulation of postsynaptic density organization postsynapse organization organelle assembly postsynaptic specialization assembly postsynapse assembly regulation of postsynapse organization regulation of organelle organization excitatory synapse assembly organelle organization regulation of organelle assembly postsynaptic specialization organization postsynaptic density assembly regulation of postsynaptic density assembly positive regulation of nervous system development positive regulation of cellular component organization positive regulation of biological process positive regulation of developmental process positive regulation of cellular process positive regulation of cellular component biogenesis positive regulation of cell junction assembly positive regulation of multicellular organismal process positive regulation of synapse assembly trans-synaptic signaling synaptic signaling signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission cell communication protein localization establishment of protein localization cellular localization nitrogen compound transport transport secretion organic substance transport establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region localization secretion by cell protein transport cellular macromolecule localization macromolecule localization regulation of presynapse assembly regulation of presynapse organization presynapse organization presynapse assembly cellular response to stimulus regulation of postsynaptic membrane potential system process response to stimulus modulation of chemical synaptic transmission regulation of system process regulation of signal transduction chemical synaptic transmission, postsynaptic modulation of excitatory postsynaptic potential signal transduction 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 negative regulation of excitatory postsynaptic potential regulation of cell communication excitatory postsynaptic potential regulation of membrane potential heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules cell adhesion cell-cell adhesion cell-cell adhesion via plasma-membrane adhesion molecules cerebellar cortex morphogenesis cellular developmental process hindbrain morphogenesis neurogenesis central nervous system neuron differentiation cerebellar granular layer morphogenesis neuron differentiation cell differentiation metencephalon development cerebellar cortex formation cerebellum morphogenesis head development animal organ development brain development cerebellar granular layer development glutamatergic neuron differentiation generation of neurons cerebellar cortex development anatomical structure morphogenesis cerebellum development central nervous system development cerebellar granule cell differentiation anatomical structure formation involved in morphogenesis hindbrain development cerebellar granular layer formation cell differentiation in hindbrain negative regulation of signaling negative regulation of synaptic transmission negative regulation of cell communication positive regulation of long-term synaptic depression regulation of synaptic plasticity long-term synaptic depression regulation of long-term synaptic depression maintenance of synapse structure cell junction maintenance cellular component maintenance establishment of localization in cell neuron apoptotic process regulation of apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death regulation of neuron apoptotic process glutamate receptor signaling pathway startle response regulation of response to external stimulus neuromuscular process negative regulation of response to stimulus prepulse inhibition response to external stimulus negative regulation of response to external stimulus regulation of neuron projection development cell projection organization cell development neuron projection development plasma membrane bounded cell projection organization regulation of cell projection organization neuron development regulation of plasma membrane bounded cell projection organization synaptic transmission, glutamatergic	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane extracellular region extracellular matrix external encapsulating structure collagen-containing extracellular matrix cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane extracellular region extracellular matrix external encapsulating structure collagen-containing extracellular matrix parallel fiber to Purkinje cell synapse excitatory synapse synaptic cleft glutamatergic synapse postsynaptic specialization membrane postsynaptic specialization postsynaptic density membrane postsynaptic density neuron to neuron synapse organelle asymmetric synapse protein-containing complex plasma membrane protein complex membrane protein complex transporter complex receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection dendrite dendritic tree

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A	IPR001073	C1q domain	Domain
A	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A	IPR015683	Ionotropic glutamate receptor	Family
A	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A	IPR001828	Receptor, ligand binding region	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O43424	allergic rhinitis medulloblastoma glioblastoma psoriasis malignant ependymoma subependymal giant cell astrocytoma autosomal recessive spinocerebellar ataxia 18 Ataxias, Hereditary cerebellar ataxia neurodegenerative disease spinocerebellar ataxia type 2 spinocerebellar ataxia type 6 autosomal dominant cerebellar ataxia colorectal cancer psoriasis allergic rhinitis medulloblastoma glioblastoma psoriasis malignant ependymoma subependymal giant cell astrocytoma autosomal recessive spinocerebellar ataxia 18 Ataxias, Hereditary cerebellar ataxia neurodegenerative disease spinocerebellar ataxia type 2 spinocerebellar ataxia type 6 autosomal dominant cerebellar ataxia colorectal cancer psoriasis spinocerebellar ataxia type 4 spinocerebellar ataxia type 7 intellectual disability spinocerebellar ataxia type 1 spinocerebellar ataxia type 5

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.