[English] 日本語
Yorodumi
- PDB-5jei: Crystal structure of the GluA2 LBD in complex with FW -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jei
TitleCrystal structure of the GluA2 LBD in complex with FW
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsTRANSPORT PROTEIN / ligand binding domain / glutamate receptor 2
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / immunoglobulin binding / Trafficking of GluR2-containing AMPA receptors / response to lithium ion ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / immunoglobulin binding / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / response to fungicide / regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / cytoskeletal protein binding / ionotropic glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / presynaptic active zone membrane / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / dendrite cytoplasm / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / cerebral cortex development / Schaffer collateral - CA1 synapse / receptor internalization / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ETE / Chem-FWD / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.229 Å
AuthorsEibl, C. / Salazar, H. / Chebli, M. / Plested, A.J.R.
Funding support Germany, Austria, France, 4items
OrganizationGrant numberCountry
German Research FoundationPL619.1 Germany
European Research Council647895 Germany
Austrian Science FundJ3682-B21 Austria
HFSP France
CitationJournal: Nat Commun / Year: 2017
Title: Mechanism of partial agonism in AMPA-type glutamate receptors.
Authors: Salazar, H. / Eibl, C. / Chebli, M. / Plested, A.
History
DepositionApr 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,18315
Polymers29,2831
Non-polymers1,90014
Water6,756375
1
A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,73060
Polymers117,1314
Non-polymers7,59956
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation1_545x,y-1,z1
Buried area9210 Å2
ΔGint-16 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.465, 44.425, 47.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Glutamate receptor 2,Glutamate receptor 2 / 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: 29282.744 Da / Num. of mol.: 1 / Mutation: V154C,V154C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: P19491

-
Non-polymers , 10 types, 389 molecules

#2: Chemical ChemComp-FWD / 2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID / FLUORO-WILLARDIINE


Mass: 217.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8FN3O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#7: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#8: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20O5
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 50.0 % v/v PEG 200, 200 mM Sodium Chloride, 100 mM Sodium/Potassium Phosphate pH 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2014 / Details: mirror
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.229→32.374 Å / Num. obs: 75826 / % possible obs: 96.7 % / Redundancy: 4.07 % / CC1/2: 0.999 / Rpim(I) all: 0.069 / Net I/σ(I): 14.52
Reflection shellResolution: 1.229→1.3 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.26 / % possible all: 92.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTJ

1ftj


Resolution: 1.229→32.374 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.1
RfactorNum. reflection% reflectionSelection details
Rfree0.1473 3791 5 %random selection
Rwork0.1207 ---
obs0.122 75826 96.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.229→32.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 118 375 2541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122220
X-RAY DIFFRACTIONf_angle_d1.4922949
X-RAY DIFFRACTIONf_dihedral_angle_d16.137865
X-RAY DIFFRACTIONf_chiral_restr0.086312
X-RAY DIFFRACTIONf_plane_restr0.008361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2291-1.24470.25971290.21672445X-RAY DIFFRACTION89
1.2447-1.26110.2181330.20112538X-RAY DIFFRACTION94
1.2611-1.27830.24771350.19122558X-RAY DIFFRACTION93
1.2783-1.29660.21941340.17972540X-RAY DIFFRACTION95
1.2966-1.3160.20461350.16932571X-RAY DIFFRACTION94
1.316-1.33650.1851370.16012605X-RAY DIFFRACTION96
1.3365-1.35840.18171370.15492609X-RAY DIFFRACTION95
1.3584-1.38190.21771390.15622637X-RAY DIFFRACTION96
1.3819-1.4070.20161380.14962613X-RAY DIFFRACTION96
1.407-1.43410.19471390.13132641X-RAY DIFFRACTION96
1.4341-1.46330.18951360.12292585X-RAY DIFFRACTION96
1.4633-1.49510.16141400.10882668X-RAY DIFFRACTION97
1.4951-1.52990.131410.1012672X-RAY DIFFRACTION97
1.5299-1.56820.12331390.09332640X-RAY DIFFRACTION97
1.5682-1.61060.13531410.09442677X-RAY DIFFRACTION98
1.6106-1.6580.13321410.08972690X-RAY DIFFRACTION98
1.658-1.71150.13761430.08872706X-RAY DIFFRACTION98
1.7115-1.77270.12121410.09122683X-RAY DIFFRACTION98
1.7727-1.84360.11871420.09312701X-RAY DIFFRACTION98
1.8436-1.92750.1151430.0892726X-RAY DIFFRACTION98
1.9275-2.02910.12171430.09072702X-RAY DIFFRACTION98
2.0291-2.15620.12051430.09012724X-RAY DIFFRACTION98
2.1562-2.32270.11041460.09212766X-RAY DIFFRACTION99
2.3227-2.55630.13041450.10422766X-RAY DIFFRACTION99
2.5563-2.9260.14361470.1192798X-RAY DIFFRACTION99
2.926-3.68570.13871490.13592816X-RAY DIFFRACTION99
3.6857-32.38540.16721550.15322958X-RAY DIFFRACTION98

+
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