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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUCAGON-LIKE PEPTIDE-1 IN COMPLEX WITH THE EXTRACELLULAR DOMAIN OF THE GLUCAGON-LIKE PEPTIDE-1 RECEPTOR
 
Authors :  S. Reedtz-Runge
Date :  14 Aug 09  (Deposition) - 27 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Receptor-Ligand Complex, Cell Membrane, Disulfide Bond, G-Protein Coupled Receptor, Glycoprotein, Membrane, Receptor, Transducer, Transmembrane, Amidation, Cleavage On Pair Of Basic Residues, Hormone, Secreted, Signaling Protein-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. R. Underwood, P. Garibay, L. B. Knudsen, S. Hastrup, G. H. Peters, R. Rudolph, S. Reedtz-Runge
Crystal Structure Of Glucagon-Like Peptide-1 In Complex Wit The Extracellular Domain Of The Glucagon-Like Peptide-1 Receptor
J. Biol. Chem. V. 285 723 2010
PubMed-ID: 19861722  |  Reference-DOI: 10.1074/JBC.M109.033829

(-) Compounds

Molecule 1 - GLUCAGON-LIKE PEPTIDE 1 RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL EXTRACELLULAR DOMAIN, UNP RESIDUES 24-145
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGLP-1 RECEPTOR, GLP-1-R, GLP-1R
 
Molecule 2 - GLUCAGON
    ChainsB
    EngineeredYES
    FragmentUNP RESIDUES 98-128
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHIS PEPTIDE HAS BEEN CHEMICALLY SYNTHESIZED
    SynonymGLP-1, GLUCAGON-LIKE PEPTIDE 1, GLICENTIN, GLICENTIN-RELATED POLYPEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
110M1Ligand/IonDECYL 4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D-GLUCOPYRANOSIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:101 , LEU A:111 , ASP A:114 , TRP A:120 , ASP A:122 , THR B:13 , VAL B:16 , SER B:17BINDING SITE FOR RESIDUE 10M A 1

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:46 -A:71
2A:62 -A:104
3A:85 -A:126

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IOL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014596A115VGLUC_HUMANPolymorphism5650BA24V
2UniProtVAR_018926R44HGLP1R_HUMANPolymorphism2295006AR44H

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F2_3PS50227 G-protein coupled receptors family 2 profile 1.GLP1R_HUMAN45-130  1A:45-128
2G_PROTEIN_RECEP_F2_1PS00649 G-protein coupled receptors family 2 signature 1.GLP1R_HUMAN62-86  1A:62-86

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003732561ENSE00001459910chr6:39016574-39016694121GLP1R_HUMAN1-26260--
1.2ENST000003732562ENSE00000750428chr6:39024173-3902426997GLP1R_HUMAN27-59331A:29-5931
1.3ENST000003732563ENSE00000750429chr6:39025248-39025355108GLP1R_HUMAN59-95371A:59-9537
1.4ENST000003732564ENSE00000750430chr6:39033487-39033605119GLP1R_HUMAN95-134401A:95-12834
1.5ENST000003732565ENSE00000750431chr6:39033973-39034079107GLP1R_HUMAN135-170360--
1.6ENST000003732566ENSE00000750432chr6:39040638-39040791154GLP1R_HUMAN170-221520--
1.7ENST000003732567ENSE00000750433chr6:39041386-39041545160GLP1R_HUMAN222-275540--
1.8ENST000003732568ENSE00000750434chr6:39046098-3904615861GLP1R_HUMAN275-295210--
1.9ENST000003732569ENSE00000750435chr6:39046733-3904680270GLP1R_HUMAN295-318240--
1.10ENST0000037325610ENSE00000750436chr6:39046888-3904697689GLP1R_HUMAN319-348300--
1.11ENST0000037325611ENSE00000750438chr6:39047340-39047478139GLP1R_HUMAN348-394470--
1.12ENST0000037325612ENSE00000750439chr6:39048474-3904851542GLP1R_HUMAN395-408140--
1.13ENST0000037325613ENSE00001027349chr6:39053682-390555191838GLP1R_HUMAN409-463550--

2.1bENST000003754971bENSE00001527920chr2:163008757-16300866890GLUC_HUMAN-00--
2.2aENST000003754972aENSE00002195895chr2:163005697-163005597101GLUC_HUMAN1-31310--
2.4bENST000003754974bENSE00000779529chr2:163004024-163003863162GLUC_HUMAN31-85550--
2.5aENST000003754975aENSE00000779528chr2:163002187-163002050138GLUC_HUMAN85-131471B:10-3526
2.6bENST000003754976bENSE00000779527chr2:163000680-163000537144GLUC_HUMAN131-179490--
2.7ENST000003754977ENSE00001686821chr2:163000421-1630004157GLUC_HUMAN179-18020--

(-) 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:100
 aligned with GLP1R_HUMAN | P43220 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:100
                                    38        48        58        68        78        88        98       108       118       128
          GLP1R_HUMAN    29 TVSLWETVQKWREYRRQCQRSLTEDPPPATDLFCNRTFDEYACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLQKDNSSLPWRDLSECEE 128
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh...........ee....ee......eeeeee......hhhhh...eeeeee..................hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------H------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------G_PROTEIN_RECEP_F2_3  PDB: A:45-128 UniProt: 45-130                                  PROSITE (1)
                PROSITE (2) ---------------------------------G_PROTEIN_RECEP_F2_1     ------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:29-59         -----------------------------------Exon 1.4  PDB: A:95-128            Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.3  PDB: A:59-95 UniProt: 59-95--------------------------------- Transcript 1 (2)
                 3iol A  29 TVSLWETVQKWREYRRQCQRSLTEDPPPATDLFCNRTFDEYACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLQKDNSSLPWRDLSECEE 128
                                    38        48        58        68        78        88        98       108       118       128

Chain B from PDB  Type:PROTEIN  Length:26
 aligned with GLUC_HUMAN | P01275 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:26
                                   110       120      
           GLUC_HUMAN   101 GTFTSDVSSYLEGQAAKEFIAWLVKG 126
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------V----------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
               Transcript 2 Exon 2.5a  PDB: B:10-35    Transcript 2
                 3iol B  10 GTFTSDVSSYLEGQAAKEFIAWLVKG  35
                                    19        29      

   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 3IOL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (50, 56)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLP1R_HUMAN | P43220)
molecular function
    GO:0008528    G-protein coupled peptide receptor activity    Combining with a peptide 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: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:0004967    glucagon receptor activity    Combining with glucagon 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: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.
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
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:0007190    activation of adenylate cyclase activity    Any process that initiates the activity of the inactive enzyme adenylate cyclase.
    GO:0019933    cAMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0071377    cellular response to glucagon stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.
    GO:0007611    learning or memory    The acquisition and processing of information and/or the storage and retrieval of this information over time.
    GO:0045777    positive regulation of blood pressure    Any process in which the force of blood traveling through the circulatory system is increased.
    GO:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:0008016    regulation of heart contraction    Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body.
    GO:0050796    regulation of insulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of insulin.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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.

Chain B   (GLUC_HUMAN | P01275)
molecular function
    GO:0031769    glucagon receptor binding    Interacting selectively and non-covalently with a glucagon receptor.
    GO:0005179    hormone activity    The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
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:0007188    adenylate cyclase-modulating 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 through activation or inhibition of adenylyl cyclase activity and a subsequent change in the concentration of cyclic AMP (cAMP).
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071377    cellular response to glucagon stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.
    GO:0007631    feeding behavior    Behavior associated with the intake of food.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0032099    negative regulation of appetite    Any process that reduces appetite.
    GO:1900118    negative regulation of execution phase of apoptosis    Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis.
    GO:2001243    negative regulation of intrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0030819    positive regulation of cAMP biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0090280    positive regulation of calcium ion import    Any process that increases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.
    GO:0035948    positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of gluconeogenesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0051571    positive regulation of histone H3-K4 methylation    Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
    GO:0035774    positive regulation of insulin secretion involved in cellular response to glucose stimulus    Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
    GO:0033138    positive regulation of peptidyl-serine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0010800    positive regulation of peptidyl-threonine phosphorylation    Any process that increases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:0010737    protein kinase A signaling    A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase A, which occurs as a result of a single trigger reaction or compound.
    GO:0050796    regulation of insulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of insulin.
    GO:0042594    response to starvation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
    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:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0034774    secretory granule lumen    The volume enclosed by the membrane of a secretory granule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLP1R_HUMAN | P432203c59 3c5t 4zgm 5e94 5nx2 5vew 5vex
        GLUC_HUMAN | P012751bh0 1d0r 1nau 2g49 2l63 2l64 2m5p 2m5q 4apd 4zgm 5vai

(-) Related Entries Specified in the PDB File

3c59 THE SAME PROTEIN IN COMPLEX WITH THE ANTAGONIST (SEMET14, 21)-EXENDIN-4(9-39)
3c5t THE SAME PROTEIN IN COMPLEX WITH THE ANTAGONIST EXENDIN- 4(9-39)