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(-) Description

Title :  CRYSTAL STRUCTURE OF METABOTROPIC GLUTAMATE RECEPTOR 3 PRECURSOR IN PRESENCE OF LY341495 ANTAGONIST
 
Authors :  A. K. Wernimont, A. Dong, A. Seitova, L. Crombet, G. Khutoreskaya, A. M. C. H. Arrowsmith, C. Bountra, J. Weigelt, D. Cossar, E. Dobrovetsky, S Genomics Consortium (Sgc)
Date :  27 Jun 11  (Deposition) - 27 Jul 11  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Cell Membrane, G-Protein Coupled Receptor, Glycoprotein, Membrane, Olfaction, Phosphoprotein, Receptor, Sensory Transduction, Transducer, Transmembrane, Transmembrane Helix, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Wernimont, A. Dong, A. Seitova, L. Crombet, G. Khutoreskaya, A. M. Edwards, C. H. Arrowsmith, C. Bountra, J. Weigelt, D. Cossar, E. Dobrovetsky
Crystal Structure Of Metabotropic Glutamate Receptor 3 Precursor In Presence Of Ly341495 Antagonist
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METABOTROPIC GLUTAMATE RECEPTOR 3
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFHMSP-LIC-C
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneGPRC1C, GRM3, MGLUR3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMGLUR3

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO45Ligand/IonSULFATE ION
3Z991Ligand/Ion2-[(1S,2S)-2-CARBOXYCYCLOPROPYL]-3-(9H-XANTHEN-9-YL)-D-ALANINE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO410Ligand/IonSULFATE ION
3Z992Ligand/Ion2-[(1S,2S)-2-CARBOXYCYCLOPROPYL]-3-(9H-XANTHEN-9-YL)-D-ALANINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:131 , ASN A:134 , ARG A:137 , HOH A:588BINDING SITE FOR RESIDUE SO4 A 480
2AC2SOFTWAREARG A:76 , ASP A:77 , THR A:78BINDING SITE FOR RESIDUE SO4 A 481
3AC3SOFTWAREARG A:252 , SER A:253 , ASP A:254BINDING SITE FOR RESIDUE SO4 A 482
4AC4SOFTWAREGLN A:281 , GLU A:282 , SER A:283BINDING SITE FOR RESIDUE SO4 A 483
5AC5SOFTWAREASP A:432 , THR A:433 , PHE A:434BINDING SITE FOR RESIDUE SO4 A 484
6AC6SOFTWAREARG A:39 , ARG A:43 , SER A:124 , TYR A:125 , SER A:126 , ALA A:147 , SER A:148 , THR A:149 , TYR A:197 , LYS A:364 , HOH A:525 , HOH A:544 , HOH A:545BINDING SITE FOR RESIDUE Z99 A 485
7AC7SOFTWARETHR A:73 , SER A:124 , TYR A:125 , VAL A:128BINDING SITE FOR RESIDUE CL A 486

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:32 -A:74
2A:336 -A:348
3A:387 -A:394

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:122 -Gly A:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049274G475DGRM3_HUMANPolymorphism17161026AG450D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049274G475DGRM3_HUMANPolymorphism17161026AG450D

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F3_1PS00979 G-protein coupled receptors family 3 signature 1.GRM3_HUMAN157-175  1A:132-150
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F3_1PS00979 G-protein coupled receptors family 3 signature 1.GRM3_HUMAN157-175  2A:132-150

(-) Exons   (3, 3)

Asymmetric Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003616691bENSE00001893578chr7:86273230-86274188959GRM3_HUMAN-00--
1.3cENST000003616693cENSE00001254415chr7:86394322-86394929608GRM3_HUMAN1-1561561A:5-131 (gaps)127
1.4bENST000003616694bENSE00001254406chr7:86415577-86416432856GRM3_HUMAN157-4422861A:132-417 (gaps)286
1.5ENST000003616695ENSE00000700691chr7:86468155-864692211067GRM3_HUMAN442-7973561A:417-475 (gaps)59
1.6ENST000003616696ENSE00001801909chr7:86479686-86479860175GRM3_HUMAN798-856590--
1.7cENST000003616697cENSE00001621224chr7:86493598-86494200603GRM3_HUMAN856-879240--

(-) Sequences/Alignments

Asymmetric 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:437
 aligned with GRM3_HUMAN | Q14832 from UniProtKB/Swiss-Prot  Length:879

    Alignment length:471
                                    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 RREIKIEGDLVLGGLFPINEKGTGTEECGRINEDRGIQRLEAMLFAIDEINKDDYLLPGVKLGVHILDTCSRDTYALEQSLEFVRASLTKVDEAEYMCPDGSYAIQENIPLLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAASRANASFTWVASDGWGAQESIIKGSEHVAYGAITLELASQPVRQFDRYFQSLNPYNNHRNPWFRDFWEQKFQCSLQNKRNHRRVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTLCPNTTKLCDAMKILDGKKLYKDYLLKINFTAPFNPNKDADSIVKFDTFGDGMGRYNVFNFQNVGGKYSYLKVGHWAETLSLDVNSIHWS 500
               SCOP domains d3sm9a_ A: automated ma tches                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeeeee..eee..-...eeee....hhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhhhhh.-----------------------..eeeee...hhhhhhhhhhhhhhhh..eee....hhhhhh......eee....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhh...eeeeeeee..--hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh....eeee......hhhhhh.........eeeee....hhhhhhhhhh..........hhhhhhhhhhh....---.....................hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhh.ee....-----..ee...........eeeeeeee....eeeeeeeee...eee.hhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F3_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3c  PDB: A:5-131 (gaps) UniProt: 1-156 [INCOMPLETE]                                                                     Exon 1.4b  PDB: A:132-417 (gaps) UniProt: 157-442                                                                                                                                                                                                                                             ---------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:417-475 (gaps) UniProt: 442-797            Transcript 1 (2)
                 3sm9 A   5 RREIKIEGDLVLGGLFPINEKGT-TEECGRINEDRGIQRLEAMLFAIDEINKDDYLLPGVKLGVHILDTCSRDTYALEQSLEFVRAS-----------------------LLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNISIATAEKVGR--IRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAASRANASFTWVASDGWGAQESIIKGSEHVAYGAITLELASQPVRQFDRYFQSLNPYNNHRNPWFRDFWEQKFQCSLQ---NHRRVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTLCPNTTKLCDAMKILDGKKLYKDYLLKINFTAPFN-----DSIVKFDTFGDGMGRYNVFNFQNVGGKYSYLKVGHWAETLSLDVNSIHWS 475
                                    14        24  | |   34        44        54        64        74        84      |  -         -         -|      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     |   - |     434       444       454       464       474 
                                                 27 |                                                            91                     115                                                                                                          224  |                                                                                                             339 343                                                                          420   426                                                 
                                                   29                                                                                                                                                                                                   227                                                                                                                                                                                                                                                        

   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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SM9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SM9)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(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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 Related Entries

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

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        GRM3_HUMAN | Q148321s8m 4xar 5cnk 5cnm

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