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- PDB-3ilu: Crystal structure of the AMPA subunit GluR2 bound to the alloster... -

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Basic information

Entry
Database: PDB / ID: 3ilu
TitleCrystal structure of the AMPA subunit GluR2 bound to the allosteric modulator, hydroflumethiazide
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / glutamate receptor / glur2 / AMPA receptor / neurotransmitter receptor / S1S2 / allosteric modulator
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / dendrite membrane / ionotropic glutamate receptor binding / glutamate-gated calcium ion channel activity / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / dendritic shaft / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / synaptic membrane / modulation of chemical synaptic transmission / establishment of protein localization / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / synaptic vesicle membrane / synaptic vesicle / signaling receptor activity / presynapse / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / synapse / 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
GLUTAMIC ACID / Chem-HFZ / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.003 Å
AuthorsAhmed, A.H. / Ptak, C.P. / Oswald, R.E.
CitationJournal: Biochemistry / Year: 2009
Title: Probing the allosteric modulator binding site of GluR2 with thiazide derivatives
Authors: Ptak, C.P. / Ahmed, A.H. / Oswald, R.E.
History
DepositionAug 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glutamate receptor 2
E: Glutamate receptor 2
H: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,18714
Polymers86,4253
Non-polymers1,76211
Water11,962664
1
B: Glutamate receptor 2
E: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,83510
Polymers57,6172
Non-polymers1,2188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-9 kcal/mol
Surface area23240 Å2
MethodPISA
2
H: Glutamate receptor 2
hetero molecules

H: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7048
Polymers57,6172
Non-polymers1,0886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544x,-y-1,-z-11
Buried area1510 Å2
ΔGint-9 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.289, 114.194, 163.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 28808.297 Da / Num. of mol.: 3 / Fragment: S1S2 binding domain / Mutation: N242S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur2, Gria2, Gria2; GluR2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-HFZ / 6-(trifluoromethyl)-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide 1,1-dioxide


Mass: 331.292 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H8F3N3O4S2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-18 PEG8K, 0.1 M Na Cacodylate, 0.1-0.15 zinc acetate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 23, 2008
RadiationMonochromator: RH COATED SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 60617 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Χ2: 1.56 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2.317 / Num. unique all: 2984 / Rsym value: 0.781 / Χ2: 0.98 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3dp6

3dp6


Resolution: 2.003→23.636 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.854 / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2000 3.62 %RANDOM
Rwork0.188 ---
obs0.19 55178 90.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.003 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 85.3 Å2 / Biso mean: 30.73 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--10.583 Å2-0 Å20 Å2
2---2.274 Å2-0 Å2
3---0.959 Å2
Refinement stepCycle: LAST / Resolution: 2.003→23.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 95 664 6791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096233
X-RAY DIFFRACTIONf_angle_d1.198396
X-RAY DIFFRACTIONf_chiral_restr0.073921
X-RAY DIFFRACTIONf_plane_restr0.0041038
X-RAY DIFFRACTIONf_dihedral_angle_d15.9442336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.003-2.0530.2981270.2093364349181
2.053-2.1080.2361310.1883517364887
2.108-2.170.2351390.1813654379388
2.17-2.240.2571360.1753630376688
2.24-2.320.2431350.1883590372587
2.32-2.4130.251350.1913601373687
2.413-2.5230.2531380.1943643378188
2.523-2.6560.2191390.1893727386690
2.656-2.8220.2381430.1993801394491
2.822-3.0390.2441450.1953858400393
3.039-3.3440.2341540.1884089424397
3.344-3.8260.2031560.1684146430299
3.826-4.8140.1751590.1534211437098
4.814-23.6370.2261630.2114347451098

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