[English] 日本語
Yorodumi
- PDB-3ks9: Metabotropic glutamate receptor mGluR1 complexed with LY341495 an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ks9
TitleMetabotropic glutamate receptor mGluR1 complexed with LY341495 antagonist
ComponentsMetabotropic glutamate receptor 1
KeywordsSIGNALING PROTEIN / Glutamate Receptors / mGluR1 / Dimerization / Glutamic Acid Binding / Structural Genomics / Structural Genomics Consortium / SGC / Cell membrane / G-protein coupled receptor / Glycoprotein / Membrane / Phosphoprotein / Receptor / Transducer / Transmembrane
Function / homology
Function and homology information


G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor dimeric complex / G protein-coupled receptor homodimeric complex / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / cellular response to electrical stimulus / regulation of sensory perception of pain / G protein-coupled glutamate receptor signaling pathway / L-glutamate import across plasma membrane ...G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor dimeric complex / G protein-coupled receptor homodimeric complex / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / cellular response to electrical stimulus / regulation of sensory perception of pain / G protein-coupled glutamate receptor signaling pathway / L-glutamate import across plasma membrane / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / Neurexins and neuroligins / regulation of synaptic transmission, glutamatergic / sensory perception of pain / locomotory behavior / G protein-coupled receptor activity / postsynaptic density membrane / Schaffer collateral - CA1 synapse / Sensory perception of sweet, bitter, and umami (glutamate) taste / chemical synaptic transmission / G alpha (q) signalling events / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / dendrite / glutamatergic synapse / nucleus / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 1 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / 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, metabotropic glutamate receptor 1 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / 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. / 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
Chem-Z99 / Metabotropic glutamate receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsDobrovetsky, E. / Khutoreskaya, G. / Seitova, A. / Cossar, D. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Metabotropic glutamate receptor mglur1 complexed with LY341495 antagonist
Authors: Dobrovetsky, E. / Khutoreskaya, G. / Seitova, A. / Cossar, D. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Bochkarev, A.
History
DepositionNov 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metabotropic glutamate receptor 1
B: Metabotropic glutamate receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5768
Polymers111,3782
Non-polymers1,1986
Water11,728651
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Metabotropic glutamate receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5095
Polymers55,6891
Non-polymers8204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Metabotropic glutamate receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0673
Polymers55,6891
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.230, 96.546, 97.545
Angle α, β, γ (deg.)90.000, 106.670, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Metabotropic glutamate receptor 1 / / mGluR1


Mass: 55689.145 Da / Num. of mol.: 2 / Mutation: C254S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPRC1A, GRM1, MGLUR1 / Plasmid: pFHMSP-LIC-C / Production host: BACULOVIRUS / Strain (production host): Sf9 insect cells / References: UniProt: Q13255
#2: Chemical ChemComp-Z99 / 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine / (1S,2S)-2-[(2S)-2-amino-1-hydroxy-1-oxo-3-(9H-xanthen-9-yl)propan-2-yl]cyclopropane-1-carboxylic acid / LY-341495


Mass: 353.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19NO5 / Comment: antidepressant, antagonist*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 0.2M KSCN, protein at 5mg/mL plus 2mM LY341495. Cryoprotectant used 0.9V well solution plus 0.1V 80% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→93.44 Å / Num. obs: 109274 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Χ2: 1.405 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.933.50.55951321.166193.2
1.93-1.973.50.46952801.124196.1
1.97-2.013.60.41253511.156198.1
2.01-2.053.60.34854781.164199.3
2.05-2.093.70.29654391.205199.4
2.09-2.143.80.25554871.234199.4
2.14-2.193.80.23254431.23199.4
2.19-2.253.80.19654881.328199.6
2.25-2.323.80.17354991.274199.7
2.32-2.393.80.1554841.32199.8
2.39-2.483.80.13554751.279199.7
2.48-2.583.80.11754711.306199.9
2.58-2.73.80.09854861.328199.9
2.7-2.843.80.08755341.398199.9
2.84-3.023.70.07555161.6371100
3.02-3.253.70.06755162.015199.9
3.25-3.583.70.05855242.29199.9
3.58-4.093.70.04455261.909199.9
4.09-5.153.60.03355641.372199.9
5.15-403.70.03255811.268198.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ewk

1ewk


Resolution: 1.9→93.44 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.805 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 5456 5 %RANDOM
Rwork0.206 ---
obs0.207 109265 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.49 Å2 / Biso mean: 37.873 Å2 / Biso min: 16.84 Å2
Baniso -1Baniso -2Baniso -3
1-5.03 Å20 Å20.94 Å2
2---2.5 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 1.9→93.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6916 0 82 651 7649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227251
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9599843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4395896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4423.952334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.722151189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4571545
X-RAY DIFFRACTIONr_chiral_restr0.0840.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215551
X-RAY DIFFRACTIONr_mcbond_it0.7241.54442
X-RAY DIFFRACTIONr_mcangle_it1.36627132
X-RAY DIFFRACTIONr_scbond_it2.01332809
X-RAY DIFFRACTIONr_scangle_it3.2274.52705
LS refinement shellResolution: 1.9→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 397 -
Rwork0.315 7133 -
all-7530 -
obs--92.69 %

+
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