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(-) Description

Title :  LIGAND BINDING DOMAIN OF METABOTROPOC GLUTAMATE RECEPTOR MGLUR5 COMPLEXED WITH GLUTAMATE
 
Authors :  E. Dobrovetsky, G. Khutoreskaya, A. Seitova, D. Cossar, A. M. Edwards, C. H. Arrowsmith, C. Bountra, J. Weigelt, A. Bochkarev, Structural G Consortium (Sgc)
Date :  30 Jan 10  (Deposition) - 16 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glutamate Receptors, Mglur1, Dimerization, Glutamic Acid, Cell Membrane, G-Protein Coupled Receptor, Glycoprotein, Membrane, Receptor, Transducer, Transmembrane, Structural Genomics, Structural Genomics Consortium, Sgc, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Dobrovetsky, G. Khutoreskaya, A. Seitova, D. Cossar, A. M. Edwards C. H. Arrowsmith, C. Bountra, J. Weigelt, A. Bochkarev
Metabotropic Glutamate Receptor Mglur5 Complexed With Glutamate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METABOTROPIC GLUTAMATE RECEPTOR 5
    ChainsA, B
    EngineeredYES
    Expression SystemUNIDENTIFIED BACULOVIRUS
    Expression System CellSF9 INSECT CELLS
    Expression System PlasmidPFHMSP-LIC-C
    Expression System Taxid10469
    Expression System Vector TypePLASMID
    FragmentLIGAND BINDING DOMAIN
    GeneGPRC1E, GRM5, MGLUR5
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMGLUR5

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GLU2Mod. Amino AcidGLUTAMIC ACID
2MG3Ligand/IonMAGNESIUM ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:445BINDING SITE FOR RESIDUE NAG B 1
2AC2SOFTWAREASN A:445 , LEU A:455BINDING SITE FOR RESIDUE NAG A 1
3AC3SOFTWARETYR A:64 , TRP A:100 , SER A:151 , SER A:152 , SER A:173 , ALA A:174 , THR A:175 , TYR A:223 , ASP A:305 , LYS A:396 , HOH A:509BINDING SITE FOR RESIDUE GLU A 506
4AC4SOFTWAREILE A:79 , ASP A:82 , LEU A:85 , LEU A:86 , HOH A:539BINDING SITE FOR RESIDUE MG A 507
5AC5SOFTWARELEU A:179 , LYS A:182 , PHE A:188 , ASN A:459 , GLY A:460 , ASP A:461BINDING SITE FOR RESIDUE MG A 508
6AC6SOFTWAREILE B:79 , ASN B:80 , ASP B:82 , LEU B:85 , LEU B:86BINDING SITE FOR RESIDUE MG B 506
7AC7SOFTWAREHOH B:8 , TYR B:64 , SER B:151 , SER B:152 , SER B:173 , ALA B:174 , THR B:175 , TYR B:223 , ASP B:305 , LYS B:396 , HOH B:522BINDING SITE FOR RESIDUE GLU B 507

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:57 -A:99
2A:276 -A:278
3A:365 -A:381
4A:419 -A:426
5B:57 -B:99
6B:276 -B:278
7B:365 -B:381
8B:419 -B:426

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Val A:49 -Asp A:50
2Arg A:114 -Asp A:115
3Gly A:148 -Pro A:149
4Leu A:268 -Pro A:269
5Lys A:430 -Pro A:431
6Arg B:114 -Asp B:115
7Gly B:148 -Pro B:149
8Leu B:268 -Pro B:269
9Lys B:430 -Pro B:431

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LMK)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F3_1PS00979 G-protein coupled receptors family 3 signature 1.GRM5_HUMAN158-176
 
  2A:158-176
B:158-176

(-) Exons   (0, 0)

(no "Exon" information available for 3LMK)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:438
 aligned with GRM5_HUMAN | P41594 from UniProtKB/Swiss-Prot  Length:1212

    Alignment length:471
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494 
           GRM5_HUMAN    25 RRVVAHMPGDIIIGALFSVHHQPTVDKVHERKCGAVREQYGIQRVEAMLHTLERINSDPTLLPNITLGCEIRDSCWHSAVALEQSIEFIRDSLISSEEEEGLVRCVDGSSSSFRSKKPIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSMDLSDKTLFKYFMRVVPSDAQQARAMVDIVKRYNWTYVSAVHTEGNYGESGMEAFKDMSAKEGICIAHSYKIYSNAGEQSFDKLLKKLTSHLPKARVVACFCEGMTVRGLLMAMRRLGLAGEFLLLGSDGWADRYDVTDGYQREAVGGITIKLQSPDVKWFDDYYLKLRPETNHRNPWFQEFWQHRFQCRLEGFPQENSKYNKTCNSSLTLKTHHVQDSKMGFVINAIYSMAYGLHNMQMSLCPGYAGLCDAMKPIDGRKLLESLMKTNFTGVSGDTILFDENGDSPGRYEIMNFKEMGKDYFDYINVGSWDNGELKMD 495
               SCOP domains d3lmka_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...eeeeeee.......................hhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhhh..-------------------------..eeeee...hhhhhhhhhhhhhhhh..eee....hhhhhh......eee...hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.....eeee......hhhhhh.hhhhhh..eeeee....hhhhhhhhhh..........hhhhhhhhhhh.....--------..................hhhhhhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhhh..eee.....eee..........eeeeeeee.....eeeeeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F3_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lmk A  25 RRVVAHMPGDIIIGALFSVHHQPTVDKVHERKCGAVREQYGIQRVEAMLHTLERINSDPTLLPNITLGCEIRDSCWHSAVALEQSIEFIRD-------------------------KPIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSMDLSDKTLFKYFMRVVPSDAQQARAMVDIVKRYNWTYVSAVHTEGNYGESGMEAFKDMSAKEGISIAHSYKIYSNAGEQSFDKLLKKLTSHLPKARVVACFCEGMTVRGLLMAMRRLGLAGEFLLLGSDGWADRYDVTDGYQREAVGGITIKLQSPDVKWFDDYYLKLRPETNHRNPWFQEFWQHRFQCRLEG--------NKTCNSSLTLKTHHVQDSKMGFVINAIYSMAYGLHNMQMSLCPGYAGLCDAMKPIDGRKLLESLMKTNFTGVSGDTILFDENGDSPGRYEIMNFKEMGKDYFDYINVGSWDNGELKMD 495
                                    34        44        54        64        74        84        94       104       114|        -         -      |144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364    |    -   |   384       394       404       414       424       434       444       454       464       474       484       494 
                                                                                                                    115                       141                                                                                                                                                                                                                                 369      378                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:439
 aligned with GRM5_HUMAN | P41594 from UniProtKB/Swiss-Prot  Length:1212

    Alignment length:470
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495
           GRM5_HUMAN    26 RVVAHMPGDIIIGALFSVHHQPTVDKVHERKCGAVREQYGIQRVEAMLHTLERINSDPTLLPNITLGCEIRDSCWHSAVALEQSIEFIRDSLISSEEEEGLVRCVDGSSSSFRSKKPIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSMDLSDKTLFKYFMRVVPSDAQQARAMVDIVKRYNWTYVSAVHTEGNYGESGMEAFKDMSAKEGICIAHSYKIYSNAGEQSFDKLLKKLTSHLPKARVVACFCEGMTVRGLLMAMRRLGLAGEFLLLGSDGWADRYDVTDGYQREAVGGITIKLQSPDVKWFDDYYLKLRPETNHRNPWFQEFWQHRFQCRLEGFPQENSKYNKTCNSSLTLKTHHVQDSKMGFVINAIYSMAYGLHNMQMSLCPGYAGLCDAMKPIDGRKLLESLMKTNFTGVSGDTILFDENGDSPGRYEIMNFKEMGKDYFDYINVGSWDNGELKMD 495
               SCOP domains d3lmkb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------ANF_receptor-3lmkB01 B:67-472                                                                                                                                                                                                                                                                                                                                                                                         ----------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------ANF_receptor-3lmkB02 B:67-472                                                                                                                                                                                                                                                                                                                                                                                         ----------------------- Pfam domains (2)
         Sec.struct. author ...eee...eeeeeee.......................hhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhhh..-------------------------..eeeee...hhhhhhhhhhhhhhhh..eee....hhhhhh......eee...hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh......eeee......hhhhhh.hhhhhh..eeeee....hhhhhhhhh...........hhhhhhhhhhh.....------....................hhhhhhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhhhh.eee.....eee..........eeeeeeee.....eeeeeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F3_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lmk B  26 RVVAHMPGDIIIGALFSVHHQPTVDKVHERKCGAVREQYGIQRVEAMLHTLERINSDPTLLPNITLGCEIRDSCWHSAVALEQSIEFIRD-------------------------KPIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSMDLSDKTLFKYFMRVVPSDAQQARAMVDIVKRYNWTYVSAVHTEGNYGESGMEAFKDMSAKEGISIAHSYKIYSNAGEQSFDKLLKKLTSHLPKARVVACFCEGMTVRGLLMAMRRLGLAGEFLLLGSDGWADRYDVTDGYQREAVGGITIKLQSPDVKWFDDYYLKLRPETNHRNPWFQEFWQHRFQCRLEG------KYNKTCNSSLTLKTHHVQDSKMGFVINAIYSMAYGLHNMQMSLCPGYAGLCDAMKPIDGRKLLESLMKTNFTGVSGDTILFDENGDSPGRYEIMNFKEMGKDYFDYINVGSWDNGELKMD 495
                                    35        45        55        65        75        85        95       105       115         -         -     | 145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365   |     -|      385       395       405       415       425       435       445       455       465       475       485       495
                                                                                                                   115                       141                                                                                                                                                                                                                                 369    376                                                                                                                       

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LMK)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GRM5_HUMAN | P41594)
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: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: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:0007216    G-protein coupled glutamate receptor signaling pathway    A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. Ends with regulation of a downstream cellular process, e.g. transcription.
    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: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:0050890    cognition    The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
    GO:0007612    learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:0007206    phospholipase C-activating 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 activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG).
    GO:0007205    protein kinase C-activating G-protein coupled receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of protein kinase C (PKC). PKC is activated by second messengers including diacylglycerol (DAG).
    GO:0048169    regulation of long-term neuronal synaptic plasticity    A process that modulates long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRM5_HUMAN | P415944oo9 5cgc 5cgd

(-) Related Entries Specified in the PDB File

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