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- PDB-5jei: Crystal structure of the GluA2 LBD in complex with FW -

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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 / 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 / glutamate-gated receptor activity / presynaptic active zone membrane / 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 / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / 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 / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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 / Phosphate


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


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 / 2-(2-Methoxyethoxy)ethanol


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 / 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 / Water


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

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Experimental details

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Experiment

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

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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

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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

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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

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