2E4Z - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE LIGAND-BINDING REGION OF THE GROUP III METABOTROPIC GLUTAMATE RECEPTOR

Authors :   T. Muto, D. Tsuchiya, K. Morikawa, H. Jingami

Date :   17 Dec 06 (Deposition) - 27 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   G-Protein-Coupled Receptor, Neuron, Central Nerve System, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Muto, D. Tsuchiya, K. Morikawa, H. Jingami
Structures Of The Extracellular Regions Of The Group Ii/Iii Metabotropic Glutamate Receptors
Proc. Natl. Acad. Sci. Usa V. 104 3759 2007
PubMed-ID: 17360426 | Reference-DOI: 10.1073/PNAS.0611577104

Molecule 1 - METABOTROPIC GLUTAMATE RECEPTOR 7
	Chains	:	A
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HIGH FIVE
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	LIGAND-BINDING REGION, RESIDUES 33-521
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	MGLUR7, GROUP III METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 7

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:71 , ASN A:74 , SER A:157 , GLY A:158 , SER A:159 , SER A:229 , TYR A:230	BINDING SITE FOR RESIDUE MES A 1001

Asymmetric Unit

No.	Residues
1	A:67	-	A:109
2	A:374	-	A:390
3	A:430	-	A:437

(no "Cis Peptide Bond" information available for 2E4Z)

(no "SAP(SNP)/Variant" information available for 2E4Z)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F3_1	PS00979	G-protein coupled receptors family 3 signature 1.	GRM7_RAT	165-183	1	A:165-183

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F3_1	PS00979	G-protein coupled receptors family 3 signature 1.	GRM7_RAT	165-183	2	A:165-183

(no "Exon" information available for 2E4Z)

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:434
 aligned with GRM7_RAT | P35400 from UniProtKB/Swiss-Prot  Length:915

    Alignment length:472
                                    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       509  
             GRM7_RAT    40 PHSIRIEGDVTLGGLFPVHAKGPSGVPCGDIKRENGIHRLEAMLYALDQINSDPNLLPNVTLGARILDTCSRDTYALEQSLTFVQALIQKDTSDVRCTNGEPPVFVKPEKVVGVIGASGSSVSIMVANILRLFQIPQISYASTAPELSDDRRYDFFSRVVPPDSFQAQAMVDIVKALGWNYVSTLASEGSYGEKGVESFTQISKEAGGLCIAQSVRIPQERKDRTIDFDRIIKQLLDTPNSRAVVIFANDEDIKQILAAAKRADQVGHFLWVGSDSWGSKINPLHQHEDIAEGAITIQPKRATVEGFDAYFTSRTLENNRRNVWFAEYWEENFNCKLTISGSKKEDTDRKCTGQERIGKDSNYEQEGKVQFVIDAVYAMAHALHHMNKDLCADYRGVCPEMEQAGGKKLLKYIRHVNFNGSAGTPVMFNKNGDAPGRYDIFQYQTTNTTNPGYRLIGQWTDELQLNIEDMQW 511
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeeeee..eee......eeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhhhhhhh.-----------------....eeeee...hhhhhhhhhhhhhhh...eee....hhhhhh......eee...hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh....eeeeeee.------hhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh......eeee.......hhhhh.hhhhhh..eeeee....hhhhhhhhh...........hhhhhhhhhh...-------------....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh--...........hhhhhhhhhh...ee.....ee...........eeeeeee.......eeeeeeee...eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F3_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e4z A  40 PHSIRIEGDVTLGGLFPVHAKGPSGVPCGDIKRENGIHRLEAMLYALDQINSDPNLLPNVTLGARILDTCSRDTYALEQSLTFVQALIQ-----------------KPEKVVGVIGASGSSVSIMVANILRLFQIPQISYASTAPELSDDRRYDFFSRVVPPDSFQAQAMVDIVKALGWNYVSTLASEGSYGEKGVESFTQISKEAGGLCIAQSVRIP------TIDFDRIIKQLLDTPNSRAVVIFANDEDIKQILAAAKRADQVGHFLWVGSDSWGSKINPLHQHEDIAEGAITIQPKRATVEGFDAYFTSRTLENNRRNVWFAEYWEENFNCK-------------KCTGQERIGKDSNYEQEGKVQFVIDAVYAMAHALHHMNKDLC--YRGVCPEMEQAGGKKLLKYIRHVNFNGSAGTPVMFNKNGDAPGRYDIFQYQTTNTTNPGYRLIGQWTDELQLNIEDMQW 511
                                    49        59        69        79        89        99       109       119        |-         -      |149       159       169       179       189       199       209       219       229       239       249       | -    |  269       279       289       299       309       319       329       339       349       359       369     |   -       389       399       409       419       429|  |   439       449       459       469       479       489       499       509  
                                                                                                                  128               146                                                                                                            257    264                                                                                                            375           389                                      430  |                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                   433

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 '\|'

(no "SCOP Domain" information available for 2E4Z)

(no "CATH Domain" information available for 2E4Z)

(no "Pfam Domain" information available for 2E4Z)

Asymmetric Unit(hide GO term definitions)

Chain A (GRM7_RAT | P35400)

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:0030165	PDZ domain binding	Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
	GO:0001640	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity	Combining with glutamate and transmitting the signal across the membrane by activating the alpha-subunit of an associated heterotrimeric G-protein complex to inhibit downstream adenylate cyclase activity.
	GO:0005246	calcium channel regulator activity	Modulates the activity of a calcium channel.
	GO:0048306	calcium-dependent 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), in the presence of calcium.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0016595	glutamate binding	Interacting selectively and non-covalently with glutamate, the anion of 2-aminopentanedioic acid.
	GO:0001642	group III metabotropic glutamate receptor activity	A G-protein coupled receptor that is activated by L-AP-4 and inhibits adenylate cyclase activity.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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:0007611	learning or memory	The acquisition and processing of information and/or the storage and retrieval of this information over time.
	GO:0014050	negative regulation of glutamate secretion	Any process that stops, prevents, or reduces 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:0050896	response to stimulus	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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007608	sensory perception of smell	The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. 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.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0032279	asymmetric synapse	A type of synapse occurring between an axon and a dendritic spine or dendritic shaft. Asymmetric synapses, the most abundant synapse type in the central nervous system, involve axons that contain predominantly spherical vesicles and contain a thickened postsynaptic density. Most or all synapses of this type are excitatory.
	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:0043679	axon terminus	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0043198	dendritic shaft	Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines.
	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:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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: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:0048786	presynaptic active zone	A specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, and a specialized cortical cytoskeletal matrix.
	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.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0005791	rough endoplasmic reticulum	The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
	GO:0043195	terminal bouton	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

Asymmetric Unit
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2e4u	THE EXTRACELLULAR REGION OF THE GROUP II METABOTROPIC GLUTAMATE RECEPTOR COMPLEXED WITH L-GLUTAMATE
2e4v	THE EXTRACELLULAR REGION OF THE GROUP II METABOTROPIC GLUTAMATE RECEPTOR COMPLEXED WITH DCG-IV
2e4w	THE EXTRACELLULAR REGION OF THE GROUP II METABOTROPIC GLUTAMATE RECEPTOR COMPLEXED WITH 1S,3S-ACPD
2e4x	THE EXTRACELLULAR REGION OF THE GROUP II METABOTROPIC GLUTAMATE RECEPTOR COMPLEXED WITH 1S,3R-ACPD
2e4y	THE EXTRACELLULAR REGION OF THE GROUP II METABOTROPIC GLUTAMATE RECEPTOR COMPLEXED WITH 2R,4R-APDC

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (3, 3)

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