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(-) Description

Title :  CRYSTAL STRUCTURE OF METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 COMPLEXED WITH GLUTAMATE AND GADOLINIUM ION
 
Authors :  D. Tsuchiya, N. Kunishima, N. Kamiya, H. Jingami, K. Morikawa
Date :  21 Dec 01  (Deposition) - 13 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Signal Transduction, Neurotransmitter, G Protein Coupled Receptor, Agonist, Gadolinium Ion, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Tsuchiya, N. Kunishima, N. Kamiya, H. Jingami, K. Morikawa
Structural Views Of The Ligand-Binding Cores Of A Metabotropic Glutamate Receptor Complexed With An Antagonist And Both Glutamate And Gd3+.
Proc. Natl. Acad. Sci. Usa V. 99 2660 2002
PubMed-ID: 11867751  |  Reference-DOI: 10.1073/PNAS.052708599
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentEXTRACELLULAR LIGAND BINDING REGION
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GD2Ligand/IonGADOLINIUM ATOM
2GLU1Mod. Amino AcidGLUTAMIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GD-1Ligand/IonGADOLINIUM ATOM
2GLU2Mod. Amino AcidGLUTAMIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:74 , SER A:164 , SER A:165 , SER A:186 , ALA A:187 , THR A:188 , TYR A:236 , ASP A:318 , ARG A:323 , LYS A:409BINDING SITE FOR RESIDUE GLU A 1001
2AC2SOFTWAREGLU A:386 , ASP A:493BINDING SITE FOR RESIDUE GD A 2001
3AC3SOFTWAREGLU A:238BINDING SITE FOR RESIDUE GD A 2002

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:67 -A:109
2A:289 -A:291
3A:378 -A:394
4A:432 -A:439

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:161 -Pro A:162
2Leu A:281 -Pro A:282
3Lys A:443 -Pro A:444

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ISR)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F3_1PS00979 G-protein coupled receptors family 3 signature 1.GRM1_RAT171-189  1A:171-189
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F3_1PS00979 G-protein coupled receptors family 3 signature 1.GRM1_RAT171-189  2A:171-189

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000193191ENSRNOE00000136381chr1:5744593-574453658GRM1_RAT-00--
1.2ENSRNOT000000193192ENSRNOE00000136431chr1:5743190-57421731018GRM1_RAT1-2342341A:36-234 (gaps)199
1.3ENSRNOT000000193193ENSRNOE00000136613chr1:5615348-5615099250GRM1_RAT234-317841A:234-31784
1.4ENSRNOT000000193194ENSRNOE00000136744chr1:5417531-5417296236GRM1_RAT317-396801A:317-39680
1.5ENSRNOT000000193195ENSRNOE00000136890chr1:5381153-5380907247GRM1_RAT396-478831A:396-47883
1.6ENSRNOT000000193196ENSRNOE00000137020chr1:5375675-5375507169GRM1_RAT478-534571A:478-1001 (gaps)37
1.7ENSRNOT000000193197ENSRNOE00000278695chr1:5367325-5367199127GRM1_RAT535-577430--
1.8ENSRNOT000000193198ENSRNOE00000137296chr1:5352236-5351306931GRM1_RAT577-8873110--
1.11ENSRNOT0000001931911ENSRNOE00000137534chr1:5322394-53186173778GRM1_RAT887-11993130--

(-) 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:449
 aligned with GRM1_RAT | P23385 from UniProtKB/Swiss-Prot  Length:1199

    Alignment length:479
                                    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       505         
            GRM1_RAT     36 RSVARMDGDVIIGALFSVHHQPPAEKVPERKCGEIREQYGIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSSVALEQSIEFIRDSLISIRDEKDGLNRCLPDGQTLPPGRTKKPIAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDKTLYKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMDAFKELAAQEGLCIAHSDKIYSNAGEKSFDRLLRKLRERLPKARVVVCFCEGMTVRGLLSAMRRLGVVGEFSLIGSDGWADRDEVIEGYEVEANGGITIKLQSPEVRSFDDYFLKLRLDTNTRNPWFPEFWQHRFQCRLPGHLLENPNFKKVCTGNESLEENYVQDSKMGFVINAIYAMAHGLQNMHHALCPGHVGLCDAMKPIDGRKLLDFLIKSSFVGVSGEEVWFDEKGDAPGRYDIMNLQYTEANRYDYVHVGTWHEGVLNIDDYKIQM  514
               SCOP domains d1isra_ A: Metabotropic glutamate receptor subtype 1                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1isrA01 A:36-206,A:344-476  [code=3.40.50.2300, no name defined]                                                                                                           1isrA02 A:207-343,A:477-512  [code=3.40.50.2300, no name defined]                                                                        1isrA01 A:36-206,A:344-476  [code=3.40.50.2300, no name defined]                                                                     1isrA02 A:207-343,A:477-512          - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeeeee.......................hhhhhhhhhhhhhhhh..........eeeeeee...hhhhhhhhhhhhh.-----------------------------..eeeee...hhhhhhhhhhhhh.....eee....hhhhhh......eee....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhh.....eeee......hhhhhh..hhhhh..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 1 (1) Exon 1.2  PDB: A:36-234 (gaps) UniProt: 1-234 [INCOMPLETE]                                                                                                                                             ----------------------------------------------------------------------------------Exon 1.4  PDB: A:317-396 UniProt: 317-396                                       ---------------------------------------------------------------------------------Exon 1.6  PDB: A:478-1001 (gaps)      Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:234-317 UniProt: 234-317                                           ------------------------------------------------------------------------------Exon 1.5  PDB: A:396-478 UniProt: 396-478                                          ------------------------------------ Transcript 1 (2)
                1isr A   36 RSVARMDGDVIIGALFSVHHQPPAEKVPERKCGEIREQYGIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSSVALEQSIEFIR-----------------------------KPIAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDKTLYKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMDAFKELAAQEGLCIAHSDKIYSNAGEKSFDRLLRKLRERLPKARVVVCFCEGMTVRGLLSAMRRLGVVGEFSLIGSDGWADRDEVIEGYEVEANGGITIKLQSPEVRSFDDYFLKLRLDTNTRNPWFPEFWQHRFQCRLPGHLLENPNFKKVCTGNESLEENYVQDSKMGFVINAIYAMAHGLQNMHHALCPGHVGLCDAMKPIDGRKLLDFLIKSSFVGVSGEEVWFDEKGDAPGRYDIMNLQYTEANRYDYVHVGTWHEGVLNIDDYKI-E 1001
                                    45        55        65        75        85        95       105       115        |-         -         -       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       505      | |
                                                                                                                  124                           154                                                                                                                                                                                                                                                                                                                                                                   512 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       1001

   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A   (GRM1_RAT | P23385)
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:0001639    PLC activating G-protein coupled glutamate receptor activity    A G-protein coupled receptor that binds glutamate and is linked to the inositol 1,4,5-trisphosphate/calcium signaling system.
    GO:0030331    estrogen receptor binding    Interacting selectively and non-covalently with an estrogen receptor.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0019722    calcium-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
    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:0038042    dimeric G-protein coupled receptor signaling pathway    A series of molecular signals initiated by an extracellular signal combining with a dimeric 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. Heterodimeric and homodimeric GPCRs may have different functional properties from those of the respective monomers.
    GO:0051899    membrane depolarization    The process in which membrane potential decreases with respect to its steady-state potential, usually from negative potential to a more positive potential. For example, the initial depolarization during the rising phase of an action potential is in the direction from the negative steady-state resting potential towards the positive membrane potential that will be the peak of the action potential.
    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:0051482    positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway    Any process that increases the concentration of calcium ions in the cytosol that occurs as part of a PLC-activating G-protein coupled receptor signaling pathway. G-protein-activated PLC hydrolyses phosphatidylinositol-bisphosphate (PIP2) to release diacylglycerol (DAG) and inositol trisphosphate (IP3). IP3 then binds to calcium release channels in the endoplasmic reticulum (ER) to trigger calcium ion release into the cytosol.
    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:0014048    regulation of glutamate secretion    Any process that modulates the frequency, rate or extent of the controlled release of glutamate.
    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:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    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.
    GO:0051932    synaptic transmission, GABAergic    The vesicular release of gamma-aminobutyric acid (GABA). from a presynapse, across a chemical synapse, the subsequent activation of GABA 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.
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: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: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)

UniProtKB/Swiss-Prot
        GRM1_RAT | P233851ewk 1ewt 1ewv 1iss

(-) Related Entries Specified in the PDB File

1ewk 1EWK CONTAINS THE SAME PROTEIN COMPLEXED WITH GLUTAMATE
1ewt 1EWT CONTAINS THE SAME PROTEIN, LIGAND-FREE FORM I
1ewv 1EWV CONTAINS THE SAME PROTEIN, LIGAND-FREE FORM II
1iss 1ISS CONTAINS THE SAME PROTEIN COMPLEXED WITH ANTAGONIST.