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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE LIGAND-BOUND GLUCAGON-LIKE PEPTIDE-1 RECEPTOR EXTRACELLULAR DOMAIN

Authors :   S. Runge

Date :   01 Feb 08 (Deposition) - 19 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ligand-Bound G Protein-Coupled Receptor Extracellular Domain, G- Protein Coupled Receptor, Glycoprotein, Membrane, Transducer, Transmembrane, Amidation, Cleavage On Pair Of Basic Residues, Secreted, Signaling Protein-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Runge, H. Thogersen, K. Madsen, J. Lau, R. Rudolph
Crystal Structure Of The Ligand-Bound Glucagon-Like Peptide-1 Receptor Extracellular Domain
J. Biol. Chem. V. 283 11340 2008
PubMed-ID: 18287102 | Reference-DOI: 10.1074/JBC.M708740200

Molecule 1 - GLUCAGON-LIKE PEPTIDE 1 RECEPTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL EXTRACELLULAR DOMAIN, UNP RESIDUES 24-145
	Gene	:	GLUCAGON-LIKE PEPTIDE-1 RECEPTOR(GLP1R)
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GLP-1 RECEPTOR, GLP-1-R, GLP-1R

Molecule 2 - EXENDIN-4
	Chains	:	B
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 56-86
	Other Details	:	EXENDIN-4(9-39) WAS GENERATED BY CHEMICAL SYNTHESIS; THIS SEQUENCE OCCURS NATURALLY IN HELODERMA SUSPECTUM.
	Synonym	:	EXENATIDE
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	10M	1	Ligand/Ion	DECYL 4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D-GLUCOPYRANOSIDE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:43 , PHE A:80 , ASN A:82 , HIS A:99 , TYR A:101 , HOH A:164	BINDING SITE FOR RESIDUE 10M A 1

Asymmetric/Biological Unit

No.	Residues
1	A:46	-	A:71
2	A:62	-	A:104
3	A:85	-	A:126

Asymmetric/Biological Unit

No.	Residues
1	Ser B:32	-	Ser B:33

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018926	R	44	H	GLP1R_HUMAN	Polymorphism	2295006	A	R	44	H
2	UniProt	VAR_018927	R	131	Q	GLP1R_HUMAN	Polymorphism	3765467	A	R	131	Q

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F2_3	PS50227	G-protein coupled receptors family 2 profile 1.	GLP1R_HUMAN	45-130	1	A:45-130
2	G_PROTEIN_RECEP_F2_1	PS00649	G-protein coupled receptors family 2 signature 1.	GLP1R_HUMAN	62-86	1	A:62-86

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000373256	1	ENSE00001459910	chr6:39016574-39016694	121	GLP1R_HUMAN	1-26	26	0	-	-
1.2	ENST00000373256	2	ENSE00000750428	chr6:39024173-39024269	97	GLP1R_HUMAN	27-59	33	1	A:28-59	32
1.3	ENST00000373256	3	ENSE00000750429	chr6:39025248-39025355	108	GLP1R_HUMAN	59-95	37	1	A:59-95	37
1.4	ENST00000373256	4	ENSE00000750430	chr6:39033487-39033605	119	GLP1R_HUMAN	95-134	40	1	A:95-131	37
1.5	ENST00000373256	5	ENSE00000750431	chr6:39033973-39034079	107	GLP1R_HUMAN	135-170	36	0	-	-
1.6	ENST00000373256	6	ENSE00000750432	chr6:39040638-39040791	154	GLP1R_HUMAN	170-221	52	0	-	-
1.7	ENST00000373256	7	ENSE00000750433	chr6:39041386-39041545	160	GLP1R_HUMAN	222-275	54	0	-	-
1.8	ENST00000373256	8	ENSE00000750434	chr6:39046098-39046158	61	GLP1R_HUMAN	275-295	21	0	-	-
1.9	ENST00000373256	9	ENSE00000750435	chr6:39046733-39046802	70	GLP1R_HUMAN	295-318	24	0	-	-
1.10	ENST00000373256	10	ENSE00000750436	chr6:39046888-39046976	89	GLP1R_HUMAN	319-348	30	0	-	-
1.11	ENST00000373256	11	ENSE00000750438	chr6:39047340-39047478	139	GLP1R_HUMAN	348-394	47	0	-	-
1.12	ENST00000373256	12	ENSE00000750439	chr6:39048474-39048515	42	GLP1R_HUMAN	395-408	14	0	-	-
1.13	ENST00000373256	13	ENSE00001027349	chr6:39053682-39055519	1838	GLP1R_HUMAN	409-463	55	0	-	-

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:104
 aligned with GLP1R_HUMAN | P43220 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:104
                                    37        47        57        67        77        87        97       107       117       127    
          GLP1R_HUMAN    28 ATVSLWETVQKWREYRRQCQRSLTEDPPPATDLFCNRTFDEYACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLQKDNSSLPWRDLSECEESKR 131
               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--------------------------------------------------------------------------------------Q SAPs(SNPs)
                PROSITE (1) -----------------G_PROTEIN_RECEP_F2_3  PDB: A:45-130 UniProt: 45-130                                   - PROSITE (1)
                PROSITE (2) ----------------------------------G_PROTEIN_RECEP_F2_1     --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:28-59          -----------------------------------Exon 1.4  PDB: A:95-131 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.3  PDB: A:59-95 UniProt: 59-95------------------------------------ Transcript 1 (2)
                 3c5t A  28 ATVSLWETVQKWREYRRQCQRSLTEDPPPATDLFCNRTFDEYACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLQKDNSSLPWRDLSECEESKR 131
                                    37        47        57        67        77        87        97       107       117       127

Chain B from PDB  Type:PROTEIN  Length:25
 aligned with EXE4_HELSU | P26349 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:25
                                    65        75     
           EXE4_HELSU    56 DLSKQMEEEAVRLFIEWLKNGGPSS  80
               SCOP domains d3c5tb1 B:9-33 Exendin-4  SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 3c5t B   9 DLSKQMEEEAVRLFIEWLKNGGPSS  33
                                    18        28

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Peptides (792)

Fold: Peptide hormones (51)

Superfamily: Peptide hormones (51)

Family: Peptide hormones (51)

Protein domain: Exendin-4 (3)

Synthetic (3)

d3c5tb1

B:9-33

(no "CATH Domain" information available for 3C5T)

(no "Pfam Domain" information available for 3C5T)

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 (EXE4_HELSU | P26349)

molecular function
	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.
biological process
	GO:0008217	regulation of blood pressure	Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
cellular component
	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.

Asymmetric/Biological Unit
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	GLP1R_HUMAN \| P43220
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UniProtKB/Swiss-Prot
	EXE4_HELSU \| P26349	:	1jrj 2mj9 2nav 2naw 3c59
	GLP1R_HUMAN \| P43220	:	3c59 3iol 4zgm 5e94 5nx2 5vew 5vex

3c59	THE SAME PROTEIN IN COMPLEX WITH THE NATIVE LIGAND EXENDIN- 4(9-39)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

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Exons (3, 3)

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Gene Ontology (25, 25)

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