[English] 日本語
Yorodumi
- PDB-6xsr: Crystal structure of GluA2 AMPA receptor in complex with trans-4-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xsr
TitleCrystal structure of GluA2 AMPA receptor in complex with trans-4-butylcyclohexane carboxylic acid (4-BCCA) inhibitor
ComponentsGlutamate receptor 2GRIA2
KeywordsTRANSPORT PROTEIN / AMPA receptor / ion channels / synapse / BCCA
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / regulation of synaptic transmission, glutamatergic / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / chemical synaptic transmission / perikaryon / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
trans-4-butylcyclohexane-1-carboxylic acid / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.25 Å
AuthorsYelshanskaya, M.V. / Singh, A.K. / Sobolevsky, A.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS083660 United States
CitationJournal: Br.J.Pharmacol. / Year: 2022
Title: Structural basis of AMPA receptor inhibition by trans-4-butylcyclohexane carboxylic acid.
Authors: Yelshanskaya, M.V. / Singh, A.K. / Narangoda, C. / Williams, R.S.B. / Kurnikova, M.G. / Sobolevsky, A.I.
History
DepositionJul 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 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: Glutamate receptor 2
B: Glutamate receptor 2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,86310
Polymers362,6094
Non-polymers1,2536
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26430 Å2
ΔGint-199 kcal/mol
Surface area138500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.790, 110.400, 600.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Glutamate receptor 2 / GRIA2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 90652.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Homo sapiens (human) / References: UniProt: P19491
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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-V8G / trans-4-butylcyclohexane-1-carboxylic acid


Mass: 184.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H20O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.41 Å3/Da / Density % sol: 72.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8-11% (w/v) PEG 8,000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate (pH 6.3-6.7) or 11-14% (w/v) PEG 6,000, 0.1 M ammonium phosphate and 0.1 M TRIS (pH 7.9-8.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 21, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 4.25→48.912 Å / Num. obs: 83453 / % possible obs: 99.6 % / Redundancy: 9.82 % / CC1/2: 0.99 / Rmerge(I) obs: 0.45 / Net I/σ(I): 9.35
Reflection shellResolution: 4.25→4.52 Å / Num. unique obs: 14923 / CC1/2: 0.61

-
Processing

Software
NameVersionClassification
PHENIX(1.16_3549)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG2

3kg2


Resolution: 4.25→48.912 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2959 4184 5.01 %
Rwork0.2604 --
obs0.2622 83453 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.25→48.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23693 0 82 0 23775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224264
X-RAY DIFFRACTIONf_angle_d0.55832857
X-RAY DIFFRACTIONf_dihedral_angle_d5.68214331
X-RAY DIFFRACTIONf_chiral_restr0.0413728
X-RAY DIFFRACTIONf_plane_restr0.0044171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2502-4.29840.34081310.342541X-RAY DIFFRACTION100
4.2984-4.3490.35541430.352715X-RAY DIFFRACTION100
4.349-4.4020.38541410.35362672X-RAY DIFFRACTION100
4.402-4.45770.35881380.34982600X-RAY DIFFRACTION100
4.4577-4.51630.39571390.34932674X-RAY DIFFRACTION100
4.5163-4.57810.29811350.292623X-RAY DIFFRACTION99
4.5781-4.64340.34031440.342656X-RAY DIFFRACTION99
4.6434-4.71270.3821380.31432582X-RAY DIFFRACTION100
4.7127-4.78630.30761440.32710X-RAY DIFFRACTION100
4.7863-4.86470.37051350.31472638X-RAY DIFFRACTION100
4.8647-4.94850.31591410.30942599X-RAY DIFFRACTION100
4.9485-5.03840.35011400.30742688X-RAY DIFFRACTION100
5.0384-5.13520.33251460.30852695X-RAY DIFFRACTION100
5.1352-5.23990.34141320.3152608X-RAY DIFFRACTION100
5.2399-5.35370.271420.272643X-RAY DIFFRACTION100
5.3537-5.47810.27821440.27822667X-RAY DIFFRACTION100
5.4781-5.61490.27581390.27582611X-RAY DIFFRACTION100
5.6149-5.76650.31221410.30412731X-RAY DIFFRACTION99
5.7665-5.93590.30191360.30192571X-RAY DIFFRACTION100
5.9359-6.12710.36681500.29862718X-RAY DIFFRACTION100
6.1271-6.34570.33911330.28852601X-RAY DIFFRACTION100
6.3457-6.59910.30291440.28782667X-RAY DIFFRACTION100
6.5991-6.89870.26891400.26892650X-RAY DIFFRACTION100
6.8987-7.26130.28981410.26962659X-RAY DIFFRACTION100
7.2613-7.71460.29111390.26382614X-RAY DIFFRACTION98
7.5-100.34271360.2622623X-RAY DIFFRACTION99
7.7146-8.30760.30031350.24242625X-RAY DIFFRACTION100
7.9-100.23731370.1912632X-RAY DIFFRACTION99
8-9.13870.23551430.21022665X-RAY DIFFRACTION100

+
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