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- PDB-2e4z: Crystal structure of the ligand-binding region of the group III m... -

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Basic information

Entry
Database: PDB / ID: 2e4z
TitleCrystal structure of the ligand-binding region of the group III metabotropic glutamate receptor
ComponentsMetabotropic glutamate receptor 7
KeywordsSIGNALING PROTEIN / G-protein-coupled receptor / neuron / central nerve system
Function / homology
Function and homology information


group III metabotropic glutamate receptor activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / : / negative regulation of glutamate secretion / serine binding / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / conditioned taste aversion / G protein-coupled glutamate receptor signaling pathway / short-term memory ...group III metabotropic glutamate receptor activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / : / negative regulation of glutamate secretion / serine binding / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / conditioned taste aversion / G protein-coupled glutamate receptor signaling pathway / short-term memory / glutamate receptor activity / nervous system process / presynaptic active zone / G alpha (i) signalling events / glutamate binding / axon development / adult behavior / transmission of nerve impulse / associative learning / asymmetric synapse / multicellular organismal response to stress / behavioral fear response / regulation of synaptic transmission, glutamatergic / adenylate cyclase inhibitor activity / voltage-gated calcium channel activity / presynaptic active zone membrane / axon terminus / presynaptic modulation of chemical synaptic transmission / dendritic shaft / calcium channel regulator activity / PDZ domain binding / sensory perception of sound / GABA-ergic synapse / memory / terminal bouton / calcium-dependent protein binding / presynaptic membrane / cell cortex / chemical synaptic transmission / negative regulation of neuron apoptotic process / postsynaptic membrane / learning or memory / calmodulin binding / receptor complex / protein dimerization activity / axon / neuronal cell body / dendrite / glutamatergic synapse / cell surface / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 7 / GPCR, family 3, metabotropic glutamate receptor / : / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 3. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site ...GPCR, family 3, metabotropic glutamate receptor 7 / GPCR, family 3, metabotropic glutamate receptor / : / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 3. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Response regulator / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Metabotropic glutamate receptor 7
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMuto, T. / Tsuchiya, D. / Morikawa, K. / Jingami, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structures of the extracellular regions of the group II/III metabotropic glutamate receptors
Authors: Muto, T. / Tsuchiya, D. / Morikawa, K. / Jingami, H.
History
DepositionDec 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2262
Polymers56,0311
Non-polymers1951
Water00
1
A: Metabotropic glutamate receptor 7
hetero molecules

A: Metabotropic glutamate receptor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4524
Polymers112,0622
Non-polymers3902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Unit cell
Length a, b, c (Å)92.431, 92.431, 114.332
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the biological assembly is generated by the two fold axis: X-Y,-Y,-1/3-Z

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Components

#1: Protein Metabotropic glutamate receptor 7 / mGluR7 / group III metabotropic glutamate receptor subtype 7


Mass: 56030.871 Da / Num. of mol.: 1 / Fragment: ligand-binding region, residues 33-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): HIGH FIVE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35400
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.02M Citrate, 0.08M MES, 0.01M Glutamate, 2.2M ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2004
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→100 Å / Num. all: 8887 / Num. obs: 8887 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.112 / Rsym value: 0.106 / Net I/σ(I): 5.4
Reflection shellResolution: 3.3→3.48 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EWK

1ewk


Resolution: 3.3→12 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.823 / SU B: 33.152 / SU ML: 0.579 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R Free: 0.702 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.32395 607 7 %RANDOM
Rwork0.26996 ---
all0.279 8036 --
obs0.27369 8036 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.703 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20.94 Å20 Å2
2--1.88 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 3.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 12 0 3305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213379
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9631.9344601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9735429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022602
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21680
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2422150
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34343432
X-RAY DIFFRACTIONr_scbond_it2.58441229
X-RAY DIFFRACTIONr_scangle_it4.09161169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.379 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 43
Rwork0.225 533
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.12320.4148-1.90974.117-0.07164.6569-0.172-0.2384-0.04460.28020.08670.2115-0.0896-0.26630.08530.3306-0.01090.01910.0006-0.00680.140238.51366.7038-0.801
23.4828-0.38510.17411.0025-4.07756.3598-0.2278-0.30340.172-0.12930.16010.11970.10160.16430.06780.22470.0444-0.05630.34930.09440.289262.9157-4.517715.2428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA40 - 2068 - 174
2X-RAY DIFFRACTION1AA343 - 477311 - 445
3X-RAY DIFFRACTION1AB1001
4X-RAY DIFFRACTION2AA207 - 342175 - 310
5X-RAY DIFFRACTION2AA478 - 511446 - 479

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