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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICAL MODEL OF METABOTROPIC GLUTAMATE RECEPTOR MGLUR3 IN OPEN FORM
 
Authors :  M. S. Belenikin, I. I. Baskin, G. Costantino, V. A. Palyulin, R. Pellicciari, N. S. Zefirov
Date :  03 Feb 04  (Deposition) - 02 Mar 04  (Release) - 02 Mar 04  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Signal Transduction, Neurotransmitter, Cns, Neuron Glutamate Receptor, Glutamate Site, Mglur3 Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. S. Belenikin, I. I. Baskin, G. Costantino, V. A. Palyulin, R. Pellicciari, N. S. Zefirov
Comparative Analysis Of The Ligand-Binding Sites Of The Metabotropic Glutamate Receptors Mglur1-Mglur8
Dokl. Biochem. Biophys. V. 386 251 2002
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METABOTROPIC GLUTAMATE RECEPTOR 3
    ChainsA
    FragmentEXTRACELLULAR LIGAND BINDING REGION
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymMGLUR3

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1S8M)

(-) Sites  (0, 0)

(no "Site" information available for 1S8M)

(-) SS Bonds  (3, 3)

Theoretical Model
No.Residues
1A:55 -A:97
2A:359 -A:371
3A:410 -A:417

(-) Cis Peptide Bonds  (3, 3)

Theoretical Model
No.Residues
1Gly A:145 -Gly A:146
2Lys A:264 -Pro A:265
3Lys A:421 -Ile A:422

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Theoretical Model (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049274G475DGRM3_HUMANPolymorphism17161026AG473D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F3_1PS00979 G-protein coupled receptors family 3 signature 1.GRM3_HUMAN157-175  1A:155-173

(-) Exons   (3, 3)

Theoretical Model (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003616691bENSE00001893578chr7:86273230-86274188959GRM3_HUMAN-00--
1.3cENST000003616693cENSE00001254415chr7:86394322-86394929608GRM3_HUMAN1-1561561A:28-154 (gaps)127
1.4bENST000003616694bENSE00001254406chr7:86415577-86416432856GRM3_HUMAN157-4422861A:155-440286
1.5ENST000003616695ENSE00000700691chr7:86468155-864692211067GRM3_HUMAN442-7973561A:440-49758
1.6ENST000003616696ENSE00001801909chr7:86479686-86479860175GRM3_HUMAN798-856590--
1.7cENST000003616697cENSE00001621224chr7:86493598-86494200603GRM3_HUMAN856-879240--

(-) Sequences/Alignments

Theoretical Model
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:445
 aligned with GRM3_HUMAN | Q14832 from UniProtKB/Swiss-Prot  Length:879

    Alignment length:470
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499
           GRM3_HUMAN    30 RREIKIEGDLVLGGLFPINEKGTGTEECGRINEDRGIQRLEAMLFAIDEINKDDYLLPGVKLGVHILDTCSRDTYALEQSLEFVRASLTKVDEAEYMCPDGSYAIQENIPLLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAASRANASFTWVASDGWGAQESIIKGSEHVAYGAITLELASQPVRQFDRYFQSLNPYNNHRNPWFRDFWEQKFQCSLQNKRNHRRVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTLCPNTTKLCDAMKILDGKKLYKDYLLKINFTAPFNPNKDADSIVKFDTFGDGMGRYNVFNFQNVGGKYSYLKVGHWAETLSLDVNSIHW 499
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeeeee..eee......eeee....hhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhhh.-------------------------..eeeeee..hhhhhhhhhhhhhhh...eee....hhhhhhhhhhh.eee...hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...eeee......hhhhhh.hhhhhh..eeeee....hhhhhhhhh...........hhhhhhhhhh.............................hhhhhhhhhhhhhhhhhhhhhhhh......hhhhh...hhhhhh................................eeeeeeeee....eeeeeeeeee..eeeee.hhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F3_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3c  PDB: A:28-154 (gaps) UniProt: 1-156 [INCOMPLETE]                                                                    Exon 1.4b  PDB: A:155-440 UniProt: 157-442                                                                                                                                                                                                                                                    --------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:440-497 UniProt: 442-797 [INCOMPLETE]     Transcript 1 (2)
                 1s8m A  28 RREIKIEGDLVLGGLFPINEKGTGTEECGRINEDRGIQRLEAMLFAIDEINKDDYLLPGVKLGVHILDTCSRDTYALEQSLEFVR-------------------------LLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAASRANASFTWVASDGWGAQESIIKGSEHVAYGAITLELASQPVRQFDRYFQSLNPYNNHRNPWFRDFWEQKFQCSLQNKRNHRRVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTLCPNTTKLCDAMKILDGKKLYKDYLLKINFTAPFNPNKDADSIVKFDTFGDGMGRYNVFNFQNVGGKYSYLKVGHWAETLSLDVNSIHW 497
                                    37        47        57        67        77        87        97       107    |    -         -         -|      147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497
                                                                                                              112                       138                                                                                                                                                                                                                                                                                                                                                                       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1S8M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1S8M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1S8M)

(-) Gene Ontology  (21, 21)

Theoretical Model(hide GO term definitions)
Chain A   (GRM3_HUMAN | Q14832)
molecular function
    GO:0004930    G-protein coupled receptor activity    Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
    GO:0005246    calcium channel regulator activity    Modulates the activity of a calcium channel.
    GO:0008066    glutamate receptor activity    Combining with glutamate and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0001641    group II metabotropic glutamate receptor activity    A G-protein coupled receptor that is activated by trans-1-aminocyclopentane-1,3-dicarboxylic acid (t-ACPD) and inhibits adenylate cyclase activity.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0007196    adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled glutamate receptor binding to its physiological ligand, where the pathway proceeds with inhibition of adenylyl cyclase and a subsequent decrease in the concentration of cyclic AMP (cAMP).
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0007194    negative regulation of adenylate cyclase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of adenylate cyclase activity.
    GO:0051966    regulation of synaptic transmission, glutamatergic    Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0042734    presynaptic membrane    A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

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    Gly A:145 - Gly A:146   [ RasMol ]  
    Lys A:264 - Pro A:265   [ RasMol ]  
    Lys A:421 - Ile A:422   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GRM3_HUMAN | Q148323sm9 4xar 5cnk 5cnm

(-) Related Entries Specified in the PDB File

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