[English] 日本語
Yorodumi
- PDB-2e4w: Crystal structure of the extracellular region of the group II met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2e4w
TitleCrystal structure of the extracellular region of the group II metabotropic glutamate receptor complexed with 1S,3S-ACPD
ComponentsMetabotropic glutamate receptor 3
KeywordsSIGNALING PROTEIN / G-PROTEIN-COUPLED RECEPTOR / NEURON / CENTRAL NERVE SYSTEM
Function / homology
Function and homology information


Class C/3 (Metabotropic glutamate/pheromone receptors) / group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / G alpha (i) signalling events / astrocyte projection / cellular response to stress / postsynaptic modulation of chemical synaptic transmission / regulation of synaptic transmission, glutamatergic / sensory perception of pain / calcium channel regulator activity ...Class C/3 (Metabotropic glutamate/pheromone receptors) / group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / G alpha (i) signalling events / astrocyte projection / cellular response to stress / postsynaptic modulation of chemical synaptic transmission / regulation of synaptic transmission, glutamatergic / sensory perception of pain / calcium channel regulator activity / modulation of chemical synaptic transmission / presynaptic membrane / scaffold protein binding / gene expression / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / glutamatergic synapse / plasma membrane
Similarity search - Function
GPCR, family 3, nine cysteines domain / GPCR, family 3, metabotropic glutamate receptor 3 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 ...GPCR, family 3, nine cysteines domain / GPCR, family 3, metabotropic glutamate receptor 3 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 / Ribbon / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(1S,3S)-1-aminocyclopentane-1,3-dicarboxylic acid / Metabotropic glutamate receptor 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Non-polymer description / Version format compliance
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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 10, 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 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metabotropic glutamate receptor 3
B: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0236
Polymers126,2352
Non-polymers7894
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.739, 97.313, 107.814
Angle α, β, γ (deg.)90.00, 92.94, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains one biological homodimer.

-
Components

#1: Protein Metabotropic glutamate receptor 3 / mGluR3 / group II metabotropic glutamate receptor subtype 3


Mass: 63117.297 Da / Num. of mol.: 2 / Fragment: Extracellular region / Mutation: N414Q, N439Q
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: P31422
#2: 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


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
#3: Chemical ChemComp-C5A / (1S,3S)-1-aminocyclopentane-1,3-dicarboxylic acid / 1S,3S-ACPD


Mass: 173.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M NH4H2PO4, 2.5-5.0% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2005
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 66923 / Num. obs: 66923 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Rsym value: 0.053 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.9 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E4U

2e4u


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 4755 -RANDOM
Rwork0.2362 ---
all0.2384 66748 --
obs0.2384 66748 98.8 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8255 0 52 295 8602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007221
X-RAY DIFFRACTIONc_angle_deg1.40006
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree: 0.3605 / Rfactor Rwork: 0.3301

+
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