[English] 日本語
Yorodumi
- PDB-6b7h: Structure of mGluR3 with an agonist -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b7h
TitleStructure of mGluR3 with an agonist
ComponentsMetabotropic glutamate receptor 3
KeywordsMEMBRANE PROTEIN/AGONIST / mGluR3 Glutamate / MEMBRANE PROTEIN-AGONIST complex
Function / homology
Function and homology information


group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / postsynaptic modulation of chemical synaptic transmission / calcium channel regulator activity / regulation of synaptic transmission, glutamatergic / G protein-coupled receptor activity ...group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / postsynaptic modulation of chemical synaptic transmission / calcium channel regulator activity / regulation of synaptic transmission, glutamatergic / G protein-coupled receptor activity / presynaptic membrane / gene expression / G alpha (i) signalling events / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / dendritic spine / postsynaptic density / axon / glutamatergic synapse / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 3 / GPCR, family 3, metabotropic glutamate receptor / G-protein coupled receptors family 3 signature 1. / 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 / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 ...GPCR, family 3, metabotropic glutamate receptor 3 / GPCR, family 3, metabotropic glutamate receptor / G-protein coupled receptors family 3 signature 1. / 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 / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Chem-CWY / Metabotropic glutamate receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsMonn, J.A. / Clawson, D.K.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Synthesis and Pharmacological Characterization of C4beta-Amide-Substituted 2-Aminobicyclo[3.1.0]hexane-2,6-dicarboxylates. Identification of (1 S,2 S,4 S,5 R,6 S)-2-Amino-4-[(3-methoxybenzoyl) ...Title: Synthesis and Pharmacological Characterization of C4beta-Amide-Substituted 2-Aminobicyclo[3.1.0]hexane-2,6-dicarboxylates. Identification of (1 S,2 S,4 S,5 R,6 S)-2-Amino-4-[(3-methoxybenzoyl)amino]bicyclo[3.1.0]hexane-2,6-dicarboxylic Acid (LY2794193), a Highly Potent and Selective mGlu3Receptor Agonist.
Authors: Monn, J.A. / Henry, S.S. / Massey, S.M. / Clawson, D.K. / Chen, Q. / Diseroad, B.A. / Bhardwaj, R.M. / Atwell, S. / Lu, F. / Wang, J. / Russell, M. / Heinz, B.A. / Wang, X.S. / Carter, J.H. ...Authors: Monn, J.A. / Henry, S.S. / Massey, S.M. / Clawson, D.K. / Chen, Q. / Diseroad, B.A. / Bhardwaj, R.M. / Atwell, S. / Lu, F. / Wang, J. / Russell, M. / Heinz, B.A. / Wang, X.S. / Carter, J.H. / Getman, B.G. / Adragni, K. / Broad, L.M. / Sanger, H.E. / Ursu, D. / Catlow, J.T. / Swanson, S. / Johnson, B.G. / Shaw, D.B. / McKinzie, D.L. / Hao, J.
History
DepositionOct 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2216
Polymers58,7771
Non-polymers1,4445
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-1 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.081, 80.081, 161.887
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Metabotropic glutamate receptor 3 / / mGluR3


Mass: 58776.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM3, GPRC1C, MGLUR3 / Production host: unidentified baculovirus / References: UniProt: Q14832

-
Sugars , 2 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 16 molecules

#4: Chemical ChemComp-CWY / (1S,2S,4S,5R,6S)-2-amino-4-[(3-methoxybenzene-1-carbonyl)amino]bicyclo[3.1.0]hexane-2,6-dicarboxylic acid


Mass: 334.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N2O6
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 100 mM Bis-Tris, pH 5.5, 17% PEG10000, 100 mM ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97973 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Sep 12, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97973 Å / Relative weight: 1
ReflectionResolution: 2.82→25.28 Å / Num. obs: 15043 / % possible obs: 99 % / Redundancy: 10.7 % / Biso Wilson estimate: 82.11 Å2 / Net I/σ(I): 7.5
Reflection shellHighest resolution: 2.82 Å

-
Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALAdata scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.22data extraction
SCALAdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→25.28 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.9137 / SU R Cruickshank DPI: 1.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.188 / SU Rfree Blow DPI: 0.302 / SU Rfree Cruickshank DPI: 0.306
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 468 3.11 %RANDOM
Rwork0.184 ---
obs0.1852 15043 99.84 %-
Displacement parametersBiso max: 212.27 Å2 / Biso mean: 80.41 Å2 / Biso min: 19.26 Å2
Baniso -1Baniso -2Baniso -3
1-6.0787 Å20 Å20 Å2
2--6.0787 Å20 Å2
3----12.1575 Å2
Refine analyzeLuzzati coordinate error obs: 0.325 Å
Refinement stepCycle: final / Resolution: 2.82→25.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 95 14 3567
Biso mean--127.58 57.28 -
Num. residues----441
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1267SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes537HARMONIC5
X-RAY DIFFRACTIONt_it3632HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion491SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4119SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3632HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4928HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion19.69
LS refinement shellResolution: 2.82→3.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2865 73 2.75 %
Rwork0.1892 2582 -
all0.1919 2655 -
obs--99.14 %
Refinement TLS params.Method: refined / Origin x: -6.6981 Å / Origin y: 95.1272 Å / Origin z: 10.5489 Å
111213212223313233
T-0.1441 Å2-0.0057 Å2-0.1131 Å2--0.321 Å20.022 Å2---0.2587 Å2
L3.3861 °20.0343 °20.225 °2-2.7134 °2-0.3737 °2--2.0126 °2
S0.0066 Å °-0.1802 Å °-0.2214 Å °0.4922 Å °-0.0543 Å °-0.2785 Å °0.1518 Å °0.3059 Å °0.0478 Å °
Refinement TLS groupSelection details: { A|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more