2E4V - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE EXTRACELLULAR REGION OF THE GROUP II METABOTROPIC GLUTAMATE RECEPTOR COMPLEXED WITH DCG-IV

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 :   2.40

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

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 3
	Chains	:	A, B
	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	:	EXTRACELLULAR REGION
	Mutation	:	YES
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	MGLUR3, GROUP II METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 3

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	2CG	2	Ligand/Ion	(1R,2R)-3-[(S)-AMINO(CARBOXY)METHYL]CYCLOPROPANE-1,2-DICARBOXYLIC ACID
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:207 , ASN A:209 , HOH A:1046	BINDING SITE FOR RESIDUE NAG A 801
2	AC2	SOFTWARE	PHE B:207 , ASN B:209	BINDING SITE FOR RESIDUE NAG B 802
3	AC3	SOFTWARE	ARG A:64 , ARG A:68 , SER A:149 , TYR A:150 , SER A:151 , ALA A:172 , SER A:173 , THR A:174 , TYR A:222 , ARG A:277 , SER A:278 , ASP A:301 , GLY A:302 , LYS A:389 , HOH A:1068	BINDING SITE FOR RESIDUE 2CG A 1001
4	AC4	SOFTWARE	ARG B:64 , ARG B:68 , SER B:149 , TYR B:150 , SER B:151 , ALA B:172 , SER B:173 , THR B:174 , TYR B:222 , ARG B:277 , SER B:278 , ASP B:301 , GLY B:302 , LYS B:389 , HOH B:2083	BINDING SITE FOR RESIDUE 2CG B 2001

Asymmetric/Biological Unit

No.	Residues
1	A:57	-	A:99
2	A:240	-	A:527
3	A:361	-	A:373
4	A:412	-	A:419
5	A:509	-	A:528
6	A:513	-	A:531
7	A:534	-	A:546
8	A:549	-	A:562
9	B:57	-	B:99
10	B:240	-	B:527
11	B:361	-	B:373
12	B:412	-	B:419
13	B:509	-	B:528
14	B:513	-	B:531
15	B:534	-	B:546
16	B:549	-	B:562

(no "Cis Peptide Bond" information available for 2E4V)

(no "SAP(SNP)/Variant" information available for 2E4V)

Asymmetric/Biological Unit (2, 4)

	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.	GRM3_RAT	157-175	2	A:157-175 B:157-175
2	G_PROTEIN_RECEP_F3_2	PS00980	G-protein coupled receptors family 3 signature 2.	GRM3_RAT	527-549	2	A:527-549 B:527-549

Asymmetric/Biological Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000007572	1	ENSRNOE00000052019	chr4:20888669-20889277	609	GRM3_RAT	1-156	156	2	A:30-156 (gaps) B:28-156 (gaps)	127 129
1.2	ENSRNOT00000007572	2	ENSRNOE00000052100	chr4:20908256-20909111	856	GRM3_RAT	157-442	286	2	A:157-442 B:157-442	286 286
1.3	ENSRNOT00000007572	3	ENSRNOE00000052180	chr4:20960761-20961827	1067	GRM3_RAT	442-797	356	2	A:442-567 B:442-567	126 126
1.4	ENSRNOT00000007572	4	ENSRNOE00000052568	chr4:20967274-20967448	175	GRM3_RAT	798-854	57	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:518
 aligned with GRM3_RAT | P31422 from UniProtKB/Swiss-Prot  Length:879

    Alignment length:538
                                    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       509       519       529       539       549       559        
             GRM3_RAT    30 RREIKIEGDLVLGGLFPINEKGTGTEECGRINEDRGIQRLEAMLFAIDEINKDNYLLPGVKLGVHILDTCSRDTYALEQSLEFVRASLTKVDEAEYMCPDGSYAIQENIPLLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAANRVNASFTWVASDGWGAQESIVKGSEHVAYGAITLELASHPVRQFDRYFQSLNPYNNHRNPWFRDFWEQKFQCSLQNKRNHRQVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTLCPNTTKLCDAMKILDGKKLYKEYLLKINFTAPFNPNKGADSIVKFDTFGDGMGRYNVFNLQQTGGKYSYLKVGHWAETLSLDVDSIHWSRNSVPTSQCSDPCAPNEMKNMQPGDVCCWICIPCEPYEYLVDEFTCMDCGPGQWPTADLSGCYNLPE 567
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeeeee..eee......eeee....hhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhhhhh..--------------------....eeeeee..hhhhhhhhhhhhhhhh..eee....hhhhhh......eee...hhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh....eeee......hhhhh..hhhhhh..eeeee....hhhhhhhhhh..........hhhhhhhhhh.............................hhhhhhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhhh..eee............eee..........eeeeeee......eeeeeeee...ee.hhhhh.hhhhh..............eeee........eeee....eeeee..eeee....eee......eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F3_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F3_2   ------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:30-156 (gaps) UniProt: 1-156 [INCOMPLETE]                                                                     Exon 1.2  PDB: A:157-442 UniProt: 157-442                                                                                                                                                                                                                                                     ----------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:442-567 UniProt: 442-797 [INCOMPLETE]                                                                         Transcript 1 (2)
                 2e4v A  30 RREIKIEGDLVLGGLFPINEKGTGTEECGRINEDRGIQRLEAMLFAIDEINKDNYLLPGVKLGVHILDTCSRDTYALEQSLEFVRASL--------------------IPLLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAANRVNASFTWVASDGWGAQESIVKGSEHVAYGAITLELASHPVRQFDRYFQSLNPYNNHRNPWFRDFWEQKFQCSLQNKRNHRQVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTLCPQTTKLCDAMKILDGKKLYKEYLLKIQFTAPFNPNKGADSIVKFDTFGDGMGRYNVFNLQQTGGKYSYLKVGHWAETLSLDVDSIHWSRNSVPTSQCSDPCAPNEMKNMQPGDVCCWICIPCEPYEYLVDEFTCMDCGPGQWPTADLSGCYNLPE 567
                                    39        49        59        69        79        89        99       109       | -         -       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       519       529       539       549       559        
                                                                                                                 117                  138

Chain B from PDB  Type:PROTEIN  Length:520
 aligned with GRM3_RAT | P31422 from UniProtKB/Swiss-Prot  Length:879

    Alignment length:540
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567
             GRM3_RAT    28 FMRREIKIEGDLVLGGLFPINEKGTGTEECGRINEDRGIQRLEAMLFAIDEINKDNYLLPGVKLGVHILDTCSRDTYALEQSLEFVRASLTKVDEAEYMCPDGSYAIQENIPLLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAANRVNASFTWVASDGWGAQESIVKGSEHVAYGAITLELASHPVRQFDRYFQSLNPYNNHRNPWFRDFWEQKFQCSLQNKRNHRQVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTLCPNTTKLCDAMKILDGKKLYKEYLLKINFTAPFNPNKGADSIVKFDTFGDGMGRYNVFNLQQTGGKYSYLKVGHWAETLSLDVDSIHWSRNSVPTSQCSDPCAPNEMKNMQPGDVCCWICIPCEPYEYLVDEFTCMDCGPGQWPTADLSGCYNLPE 567
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...eeeeeee..eee......eeee....hhhhhhhhhhhhhhhh..........eeeeeee...hhhhhhhhhhhhhhh..--------------------....eeeeee..hhhhhhhhhhhhhhhh..eee....hhhhhh......eee...hhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh....eeee.............hhhhhh..eeeee....hhhhhhhhhh..........hhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhhh...ee............ee...........eeeeeee......eeeeeeee...eee.hhhh.hhhhh..............eeee........eeee....eeeee..eeee....eee......eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F3_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F3_2   ------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:28-156 (gaps) UniProt: 1-156 [INCOMPLETE]                                                                       Exon 1.2  PDB: B:157-442 UniProt: 157-442                                                                                                                                                                                                                                                     ----------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: B:442-567 UniProt: 442-797 [INCOMPLETE]                                                                         Transcript 1 (2)
                 2e4v B  28 FMRREIKIEGDLVLGGLFPINEKGTGTEECGRINEDRGIQRLEAMLFAIDEINKDNYLLPGVKLGVHILDTCSRDTYALEQSLEFVRASL--------------------IPLLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAANRVNASFTWVASDGWGAQESIVKGSEHVAYGAITLELASHPVRQFDRYFQSLNPYNNHRNPWFRDFWEQKFQCSLQNKRNHRQVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTLCPQTTKLCDAMKILDGKKLYKEYLLKIQFTAPFNPNKGADSIVKFDTFGDGMGRYNVFNLQQTGGKYSYLKVGHWAETLSLDVDSIHWSRNSVPTSQCSDPCAPNEMKNMQPGDVCCWICIPCEPYEYLVDEFTCMDCGPGQWPTADLSGCYNLPE 567
                                    37        47        57        67        77        87        97       107       117         -         -|      147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567
                                                                                                                   117                  138

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 2E4V)

(no "CATH Domain" information available for 2E4V)

(no "Pfam Domain" information available for 2E4V)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GRM3_RAT | P31422)

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: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:0050804	modulation of chemical synaptic transmission	Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission.
	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.
cellular component
	GO:0097449	astrocyte projection	A prolongation or process extending from the soma of an astrocyte and wrapping around neurons.
	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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2e4v)

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	2e4v
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UniProtKB/Swiss-Prot
	GRM3_RAT \| P31422	:	2e4u 2e4w 2e4x 2e4y

2e4u	THE SAME PROTEIN COMPLEXED WITH L-GLUTAMATE
2e4w	THE SAME PROTEIN COMPLEXED WITH 1S,3S-ACPD
2e4x	THE SAME PROTEIN COMPLEXED WITH 1S,3R-ACPD
2e4y	THE SAME PROTEIN COMPLEXED WITH 2R,4R-APDC
2e4z	THE LIGAND-BINDING REGION OF THE GROUP III METABOTROPIC GLUTAMATE RECEPTOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (16, 16)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (3, 6)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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