5KCA | pdb_00005kca

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	Ion_trans	e5kcaA1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: Ion_trans	ECOD (v294.1)

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	This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.	Domain
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	transmitter-gated monoatomic ion channel activity glutamate receptor activity molecular transducer activity gated channel activity monoatomic ion channel activity signaling receptor activity carboxylic acid transmembrane transporter activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity AMPA glutamate receptor activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity passive transmembrane transporter activity transmitter-gated monoatomic ion channel activity glutamate receptor activity molecular transducer activity gated channel activity monoatomic ion channel activity signaling receptor activity carboxylic acid transmembrane transporter activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity AMPA glutamate receptor activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity passive transmembrane transporter activity channel activity transmembrane signaling receptor activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity protein binding binding PDZ domain binding protein domain specific binding scaffold protein binding transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential cation binding ion binding metal ion binding small molecule binding identical protein binding	developmental process multicellular organismal process nervous system development excitatory synapse assembly cellular component organization cellular component biogenesis multicellular organism development cell junction organization cellular component assembly cell junction assembly anatomical structure development cellular process synapse organization cellular component organization or biogenesis developmental process multicellular organismal process nervous system development excitatory synapse assembly cellular component organization cellular component biogenesis multicellular organism development cell junction organization cellular component assembly cell junction assembly anatomical structure development cellular process synapse organization cellular component organization or biogenesis synapse assembly system development positive regulation of nervous system development regulation of cellular process positive regulation of cellular component organization 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 regulation of synapse structure or activity regulation of synapse assembly regulation of biological quality positive regulation of cellular process regulation of multicellular organismal development regulation of biological process positive regulation of cellular component biogenesis biological regulation regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly regulation of synapse organization positive regulation of multicellular organismal process positive regulation of synapse assembly regulation of postsynaptic membrane neurotransmitter receptor levels regulation of presynapse assembly regulation of presynapse organization presynapse organization presynapse assembly neuron apoptotic process regulation of apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death regulation of neuron apoptotic process cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling glutamate receptor signaling pathway cell communication signal transduction heterophilic cell-cell adhesion cell adhesion cell-cell adhesion startle response system process nervous system process regulation of response to external stimulus neuromuscular process negative regulation of response to stimulus negative regulation of biological process prepulse inhibition response to external stimulus regulation of response to stimulus negative regulation of response to external stimulus trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of postsynaptic membrane potential chemical synaptic transmission, postsynaptic excitatory postsynaptic potential regulation of membrane potential 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 organelle organization regulation of organelle assembly postsynaptic specialization organization postsynaptic density assembly regulation of postsynaptic density assembly synaptic signaling via neuropeptide 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 negative regulation of cellular process regulation of synaptic plasticity long-term synaptic depression regulation of long-term synaptic depression 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 localization macromolecule localization intracellular protein localization negative regulation of cell junction assembly negative regulation of nervous system development inhibitory synapse assembly negative regulation of cellular component organization negative regulation of developmental process negative regulation of synapse organization negative regulation of inhibitory synapse assembly negative regulation of multicellular organismal process negative regulation of synapse assembly regulation of inhibitory synapse assembly trans-synaptic signaling, modulating synaptic transmission maintenance of synapse structure cell junction maintenance cellular component maintenance cellular localization establishment of localization in cell establishment of localization establishment of protein localization transport secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell protein transport regulation of system process regulation of signal transduction modulation of excitatory postsynaptic potential regulation of nervous system process negative regulation of excitatory postsynaptic potential	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region protein-containing complex plasma membrane protein complex membrane protein complex transporter complex AMPA glutamate receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex signaling receptor complex monoatomic ion channel complex parallel fiber to Purkinje cell synapse excitatory synapse glutamatergic synapse trans-synaptic protein complex neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection dendrite dendritic tree synaptic cleft extracellular region extracellular matrix external encapsulating structure

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
A	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A	IPR050822	Cerebellin Synaptic Organizer	Family
A	IPR001073	C1q domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P23435	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 allergic rhinitis 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 allergic rhinitis medulloblastoma glioblastoma psoriasis malignant ependymoma subependymal giant cell astrocytoma

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.