NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|392898241|ref|NP_500000|]
View 

Neurotransmitter-gated ion-channel ligand-binding domain-containing protein [Caenorhabditis elegans]

Protein Classification

ligand-gated ion channel( domain architecture ID 1903392)

ligand-gated ion channel (LIC or LGIC) is a member of a family of neurotransmitter receptors vital for communication throughout the nervous system; similar to acetylcholine receptor subunits

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LGIC_ECD super family cl28912
extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ...
 87-173 7.33e-05

extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC)); This superfamily contains the extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), type-A gamma-aminobutyric acid receptor (GABAAR) and glycine receptor (GlyR). These ligand-gated ion channels (LGICs) are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. GABAAR and GlyR are anionic channels, both mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR receptor pore, resulting in hyperpolarization of the neuron. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. These ligand-gated chloride channels are critical not only for maintaining appropriate neuronal activity, but have long been important therapeutic targets: benzodiazepines, barbiturates, some intravenous and volatile anaesthetics, alcohol, strychnine, picrotoxin, and ivermectin all derive their biological activity from acting on the inhibitory half of the Cys-loop receptor family. The ECD contains the ligand binding sites for these receptors.


The actual alignment was detected with superfamily member cd18987:

Pssm-ID: 475126 [Multi-domain]  Cd Length: 185  Bit Score: 43.05  E-value: 7.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241  87 LEVIIVMTWIDERLR--LRELQDRFSMPSEYPP--WHPSLVFA-------PPVTSK--YTTLAPtSGTVNSYNTIKTTVE 153
Cdd:cd18987   24 VDMYLRQRWTDPRLAypDRNGTDPILLPSDKFDkiWLPDLYFRneksssfHDVTTPnvLVRIFP-NGTVLYSQRLTLTLS 102

                         90       100
                 ....*....|....*....|
gi 392898241 154 CQTNAWKYPFESFTCTLSVG 173
Cdd:cd18987  103 CPMNLQKFPFDTQVCTLRLE 122
LIC super family cl42365
Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of ...
 18-232 1.13e-03

Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of Neurotransmitter Receptors TC 1.A.9)Members of the LIC family of ionotropic neurotransmitter receptors are found only in vertebrate and invertebrate animals. They exhibit receptor specificity for (1)acetylcholine, (2) serotonin, (3) glycine, (4) glutamate and (5) g-aminobutyric acid (GABA). All of these receptor channels are probably hetero- orhomopentameric. The best characterized are the nicotinic acetyl-choline receptors which are pentameric channels of a2bgd subunit composition. All subunits arehomologous. The three dimensional structures of the protein complex in both the open and closed configurations have been solved at 0.9 nm resolution.The channel protein complexes of the LIC family preferentially transport cations or anions depending on the channel (e.g., the acetylcholine receptors are cationselective while glycine receptors are anion selective). [Transport and binding proteins, Cations and iron carrying compounds]


The actual alignment was detected with superfamily member TIGR00860:

Pssm-ID: 455710 [Multi-domain]  Cd Length: 459  Bit Score: 40.85  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241   18 LLLLFYQFSLVSSISQN---------ELNELSRKFKYYHSAVRPaapdnfvsDRNGTFFNIPVEIHLLATRIV---NRNL 85
Cdd:TIGR00860   5 LLALLLFASLAAVSLAGnaksnlkevERKLLDELLKNYDARVRP--------VFGGPPVTVSFNLFLRSIMDVdekNMDY 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241   86 YLEVIIVMTWIDERLRLRELQDRFSMPSEYPP---WHPSLVFA-------PPVTSKYTTL-APTSGTVNSYNTIKTTVEC 154
Cdd:TIGR00860  77 TTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDdsiWVPDIFFYnekdarfHGITMTNVLVrIHPNGSVLYSPRITLTLAC 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241  155 QTNAWKYPFESFTCTLSVGPEG----------DETLTVAQFHDLRSHT-QKLLTNVFL----------GDYPTCSLEFIF 213
Cdd:TIGR00860 157 PMDLRNFPFDVQNCSLKFESWGyttndiklewKEQGAVQVDDSLFISLpEFELLGVYGtryctsetntGEYPCLTFSFVL 236

                         250
                  ....*....|....*....
gi 392898241  214 KSEWPRALLSSFLPSILIV 232
Cdd:TIGR00860 237 RRRPLYYLLQLYIPSILIV 255
 
Name Accession Description Interval E-value
LGIC_ECD_anion cd18987
extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels; This ...
 87-173 7.33e-05

extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels; This family contains the extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels which include type-A gamma-aminobutyric acid receptor (GABAAR), glycine receptor (GlyR), invertebrate glutamate-gated chloride channel (GluCl), and histimine-gated chloride channel (HisCl). These neurotransmitter receptors directly mediate chloride permeability and constitute one half of the Cys-loop receptor family. Receptors in this family are composed of five either identical or homologous subunits, which generate diversity in functional profiles and pharmacological preferences. GABAAR and GlyR, both mediate fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR receptor pore, resulting in hyperpolarization of the neuron. GluCl channels are found only in protostomia, but are closely related to mammalian glycine receptors (GlyRs). They have several roles in these invertebrates, including controlling locomotion and feeding, and mediating sensory inputs into behavior. Ligand-gated chloride channels are critical not only for maintaining appropriate neuronal activity, but have long been important therapeutic targets: benzodiazepines, barbiturates, some intravenous and volatile anaesthetics, alcohol, strychnine, picrotoxin, and ivermectin all derive their biological activity from acting on this inhibitory half of the Cys-loop receptor family. Many of the therapeutically useful compounds acting at Cys-loop receptors target an allosteric site. The sites in Cys-loop receptors at which these allosteric ligands bind and their structure-based mechanisms of action are largely unresolved.


Pssm-ID: 349788 [Multi-domain]  Cd Length: 185  Bit Score: 43.05  E-value: 7.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241  87 LEVIIVMTWIDERLR--LRELQDRFSMPSEYPP--WHPSLVFA-------PPVTSK--YTTLAPtSGTVNSYNTIKTTVE 153
Cdd:cd18987   24 VDMYLRQRWTDPRLAypDRNGTDPILLPSDKFDkiWLPDLYFRneksssfHDVTTPnvLVRIFP-NGTVLYSQRLTLTLS 102

                         90       100
                 ....*....|....*....|
gi 392898241 154 CQTNAWKYPFESFTCTLSVG 173
Cdd:cd18987  103 CPMNLQKFPFDTQVCTLRLE 122
LIC TIGR00860
Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of ...
 18-232 1.13e-03

Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of Neurotransmitter Receptors TC 1.A.9)Members of the LIC family of ionotropic neurotransmitter receptors are found only in vertebrate and invertebrate animals. They exhibit receptor specificity for (1)acetylcholine, (2) serotonin, (3) glycine, (4) glutamate and (5) g-aminobutyric acid (GABA). All of these receptor channels are probably hetero- orhomopentameric. The best characterized are the nicotinic acetyl-choline receptors which are pentameric channels of a2bgd subunit composition. All subunits arehomologous. The three dimensional structures of the protein complex in both the open and closed configurations have been solved at 0.9 nm resolution.The channel protein complexes of the LIC family preferentially transport cations or anions depending on the channel (e.g., the acetylcholine receptors are cationselective while glycine receptors are anion selective). [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 273305 [Multi-domain]  Cd Length: 459  Bit Score: 40.85  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241   18 LLLLFYQFSLVSSISQN---------ELNELSRKFKYYHSAVRPaapdnfvsDRNGTFFNIPVEIHLLATRIV---NRNL 85
Cdd:TIGR00860   5 LLALLLFASLAAVSLAGnaksnlkevERKLLDELLKNYDARVRP--------VFGGPPVTVSFNLFLRSIMDVdekNMDY 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241   86 YLEVIIVMTWIDERLRLRELQDRFSMPSEYPP---WHPSLVFA-------PPVTSKYTTL-APTSGTVNSYNTIKTTVEC 154
Cdd:TIGR00860  77 TTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDdsiWVPDIFFYnekdarfHGITMTNVLVrIHPNGSVLYSPRITLTLAC 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241  155 QTNAWKYPFESFTCTLSVGPEG----------DETLTVAQFHDLRSHT-QKLLTNVFL----------GDYPTCSLEFIF 213
Cdd:TIGR00860 157 PMDLRNFPFDVQNCSLKFESWGyttndiklewKEQGAVQVDDSLFISLpEFELLGVYGtryctsetntGEYPCLTFSFVL 236

                         250
                  ....*....|....*....
gi 392898241  214 KSEWPRALLSSFLPSILIV 232
Cdd:TIGR00860 237 RRRPLYYLLQLYIPSILIV 255
Neur_chan_LBD pfam02931
Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ...
 43-174 4.66e-03

Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.


Pssm-ID: 460752 [Multi-domain]  Cd Length: 215  Bit Score: 38.02  E-value: 4.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241   43 FKYYHSAVRPAApdnFVSDRngtffnIPVEIHLLATRI-----VNRNLYLEVIIVMTWIDERLRLRELQ----DRFSMPS 113
Cdd:pfam02931   9 LSGYDKLVRPVA---NGSDP------VTVSIGLYLQQIidvdeKNQDLTTNVWLRQTWTDPRLAWNPEDyggiTSLRLPS 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 392898241  114 EYpPWHPSLVFA--------PPVTSKYTTLAPTsGTVNSYNTIKTTVECQTNAWKYPFESFTCTLSVGP 174
Cdd:pfam02931  80 DK-IWKPDIVLYnkadgiheVTTPNTNVRVYYD-GTVLWSPPAIYKSSCSIDVTYFPFDEQNCSLKFGS 146
 
Name Accession Description Interval E-value
LGIC_ECD_anion cd18987
extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels; This ...
 87-173 7.33e-05

extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels; This family contains the extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels which include type-A gamma-aminobutyric acid receptor (GABAAR), glycine receptor (GlyR), invertebrate glutamate-gated chloride channel (GluCl), and histimine-gated chloride channel (HisCl). These neurotransmitter receptors directly mediate chloride permeability and constitute one half of the Cys-loop receptor family. Receptors in this family are composed of five either identical or homologous subunits, which generate diversity in functional profiles and pharmacological preferences. GABAAR and GlyR, both mediate fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR receptor pore, resulting in hyperpolarization of the neuron. GluCl channels are found only in protostomia, but are closely related to mammalian glycine receptors (GlyRs). They have several roles in these invertebrates, including controlling locomotion and feeding, and mediating sensory inputs into behavior. Ligand-gated chloride channels are critical not only for maintaining appropriate neuronal activity, but have long been important therapeutic targets: benzodiazepines, barbiturates, some intravenous and volatile anaesthetics, alcohol, strychnine, picrotoxin, and ivermectin all derive their biological activity from acting on this inhibitory half of the Cys-loop receptor family. Many of the therapeutically useful compounds acting at Cys-loop receptors target an allosteric site. The sites in Cys-loop receptors at which these allosteric ligands bind and their structure-based mechanisms of action are largely unresolved.


Pssm-ID: 349788 [Multi-domain]  Cd Length: 185  Bit Score: 43.05  E-value: 7.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241  87 LEVIIVMTWIDERLR--LRELQDRFSMPSEYPP--WHPSLVFA-------PPVTSK--YTTLAPtSGTVNSYNTIKTTVE 153
Cdd:cd18987   24 VDMYLRQRWTDPRLAypDRNGTDPILLPSDKFDkiWLPDLYFRneksssfHDVTTPnvLVRIFP-NGTVLYSQRLTLTLS 102

                         90       100
                 ....*....|....*....|
gi 392898241 154 CQTNAWKYPFESFTCTLSVG 173
Cdd:cd18987  103 CPMNLQKFPFDTQVCTLRLE 122
LIC TIGR00860
Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of ...
 18-232 1.13e-03

Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of Neurotransmitter Receptors TC 1.A.9)Members of the LIC family of ionotropic neurotransmitter receptors are found only in vertebrate and invertebrate animals. They exhibit receptor specificity for (1)acetylcholine, (2) serotonin, (3) glycine, (4) glutamate and (5) g-aminobutyric acid (GABA). All of these receptor channels are probably hetero- orhomopentameric. The best characterized are the nicotinic acetyl-choline receptors which are pentameric channels of a2bgd subunit composition. All subunits arehomologous. The three dimensional structures of the protein complex in both the open and closed configurations have been solved at 0.9 nm resolution.The channel protein complexes of the LIC family preferentially transport cations or anions depending on the channel (e.g., the acetylcholine receptors are cationselective while glycine receptors are anion selective). [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 273305 [Multi-domain]  Cd Length: 459  Bit Score: 40.85  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241   18 LLLLFYQFSLVSSISQN---------ELNELSRKFKYYHSAVRPaapdnfvsDRNGTFFNIPVEIHLLATRIV---NRNL 85
Cdd:TIGR00860   5 LLALLLFASLAAVSLAGnaksnlkevERKLLDELLKNYDARVRP--------VFGGPPVTVSFNLFLRSIMDVdekNMDY 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241   86 YLEVIIVMTWIDERLRLRELQDRFSMPSEYPP---WHPSLVFA-------PPVTSKYTTL-APTSGTVNSYNTIKTTVEC 154
Cdd:TIGR00860  77 TTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDdsiWVPDIFFYnekdarfHGITMTNVLVrIHPNGSVLYSPRITLTLAC 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241  155 QTNAWKYPFESFTCTLSVGPEG----------DETLTVAQFHDLRSHT-QKLLTNVFL----------GDYPTCSLEFIF 213
Cdd:TIGR00860 157 PMDLRNFPFDVQNCSLKFESWGyttndiklewKEQGAVQVDDSLFISLpEFELLGVYGtryctsetntGEYPCLTFSFVL 236

                         250
                  ....*....|....*....
gi 392898241  214 KSEWPRALLSSFLPSILIV 232
Cdd:TIGR00860 237 RRRPLYYLLQLYIPSILIV 255
LGIC_ECD_cation cd18989
extracellular domain (LBD) of cationic Cys-loop neurotransmitter-gated ion channels; This ...
 69-174 4.63e-03

extracellular domain (LBD) of cationic Cys-loop neurotransmitter-gated ion channels; This superfamily contains the extracellular domain (ECD) of cationic Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), and zinc-activated ligand-gated ion channel (ZAC) receptor. These ligand-gated ion channels (LGICs) are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+ and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling require is as yet unknown.


Pssm-ID: 349790 [Multi-domain]  Cd Length: 180  Bit Score: 37.73  E-value: 4.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241  69 IPVEIHLLATRI-----VNRNLYLEVIIVMTWIDERLRLRelqdrfsmPSEYPP-----------WHPSLVFAPPVTSKY 132
Cdd:cd18989    1 VNVNVSFSLYSIldldeVEQTLTLSGWLTLTWTDERLTWN--------PSDYGGitsivvpsseiWTPDIVLYNSVDSLD 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 392898241 133 TTLAPT-------SGTVNSYNTIKTTVECQTNAWKYPFESFTCTLSVGP 174
Cdd:cd18989   73 LLGDSNtlvrvssDGTVTWVPPGVLTTSCDIDVTYFPFDTQTCSLRFGS 121
Neur_chan_LBD pfam02931
Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ...
 43-174 4.66e-03

Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.


Pssm-ID: 460752 [Multi-domain]  Cd Length: 215  Bit Score: 38.02  E-value: 4.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898241   43 FKYYHSAVRPAApdnFVSDRngtffnIPVEIHLLATRI-----VNRNLYLEVIIVMTWIDERLRLRELQ----DRFSMPS 113
Cdd:pfam02931   9 LSGYDKLVRPVA---NGSDP------VTVSIGLYLQQIidvdeKNQDLTTNVWLRQTWTDPRLAWNPEDyggiTSLRLPS 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 392898241  114 EYpPWHPSLVFA--------PPVTSKYTTLAPTsGTVNSYNTIKTTVECQTNAWKYPFESFTCTLSVGP 174
Cdd:pfam02931  80 DK-IWKPDIVLYnkadgiheVTTPNTNVRVYYD-GTVLWSPPAIYKSSCSIDVTYFPFDEQNCSLKFGS 146
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH