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- PDB-8qez: Crystal structure of the AMPA receptor GluA2-L504Y-N775S ligand b... -

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Basic information

Entry
Database: PDB / ID: 8qez
TitleCrystal structure of the AMPA receptor GluA2-L504Y-N775S ligand binding domain in complex with L-glutamate and positive allosteric modulator BPAM395 at 1.55A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA RECEPTOR LIGAND-BINDING DOMAIN / GLUA2 S1S2J-L504Y-N775S / BPAM395 / POSITIVE ALLOSTERIC MODULATION
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor 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 / extracellularly glutamate-gated ion channel activity / cellular response to glycine / 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 / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / receptor internalization / terminal bouton / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / 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
ACETATE ION / CACODYLATE ION / GLUTAMIC ACID / Chem-UF5 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsDorosz, J. / Laulumaa, S. / Frydenvang, K. / Kastrup, J.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Exploring thienothiadiazine dioxides as isosteric analogues of benzo- and pyridothiadiazine dioxides in the search of new AMPA and kainate receptor positive allosteric modulators.
Authors: Francotte, P. / Bay, Y. / Goffin, E. / Colson, T. / Lesenfants, C. / Dorosz, J. / Laulumaa, S. / Fraikin, P. / de Tullio, P. / Beaufour, C. / Botez, I. / Pickering, D.S. / Frydenvang, K. / ...Authors: Francotte, P. / Bay, Y. / Goffin, E. / Colson, T. / Lesenfants, C. / Dorosz, J. / Laulumaa, S. / Fraikin, P. / de Tullio, P. / Beaufour, C. / Botez, I. / Pickering, D.S. / Frydenvang, K. / Danober, L. / Kristensen, A.S. / Kastrup, J.S. / Pirotte, B.
History
DepositionSep 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 2
B: Glutamate receptor 2
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,68332
Polymers87,9053
Non-polymers2,77829
Water14,214789
1
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,33121
Polymers58,6032
Non-polymers1,72719
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glutamate receptor 2
hetero molecules

C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,70422
Polymers58,6032
Non-polymers2,10120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Unit cell
Length a, b, c (Å)114.316, 163.416, 47.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-436-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein 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: 29301.729 Da / Num. of mol.: 3 / Mutation: L504Y,N775S
Source method: isolated from a genetically manipulated source
Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUA2. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR ...Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUA2. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 118-119). THEREFORE THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (UNP RESIDUES 413- 527 AND 653-796, NUMBERING WITH SIGNAL PEPTIDE OF 21 AMINO ACIDS) THE TWO FIRST RESIDUES (GLY, ALA) ARE CLONING REMNANTS. Engineered mutations: L504Y, N775S.,NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUA2. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 118-119). THEREFORE THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (UNP RESIDUES 413- 527 AND 653-796, NUMBERING WITH SIGNAL PEPTIDE OF 21 AMINO ACIDS) THE TWO FIRST RESIDUES (GLY, ALA) ARE CLONING REMNANTS. Engineered mutations: L504Y, N775S.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: PET-22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491

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Non-polymers , 8 types, 818 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-UF5 / 6-chloranyl-4-cyclopropyl-2,3-dihydrothieno[3,2-e][1,2,4]thiadiazine 1,1-dioxide


Mass: 264.752 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H9ClN2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15.2% PEG4000, 0.1M Zn Acetate, 0.1M Cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.55→49.17 Å / Num. obs: 129920 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Net I/σ(I): 13.1 / Num. measured all: 864426
Reflection shellResolution: 1.55→1.63 Å / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.879 / Num. measured all: 124663 / Num. unique obs: 18786 / Rpim(I) all: 0.367 / Rrim(I) all: 0.953 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→49.17 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 6588 5.07 %
Rwork0.1676 --
obs0.169 129822 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6156 0 146 789 7091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076603
X-RAY DIFFRACTIONf_angle_d0.8858922
X-RAY DIFFRACTIONf_dihedral_angle_d13.0842539
X-RAY DIFFRACTIONf_chiral_restr0.052966
X-RAY DIFFRACTIONf_plane_restr0.0061127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.26772310.26154035X-RAY DIFFRACTION100
1.57-1.590.28192570.25474037X-RAY DIFFRACTION100
1.59-1.610.27022350.24164012X-RAY DIFFRACTION100
1.61-1.630.26812230.23114062X-RAY DIFFRACTION100
1.63-1.650.25552410.23494050X-RAY DIFFRACTION100
1.65-1.670.25321910.23384061X-RAY DIFFRACTION100
1.67-1.690.28642130.25774133X-RAY DIFFRACTION100
1.69-1.720.28051890.24384041X-RAY DIFFRACTION100
1.72-1.750.26032300.23074038X-RAY DIFFRACTION100
1.75-1.770.24892070.22134083X-RAY DIFFRACTION100
1.77-1.80.26252070.20344056X-RAY DIFFRACTION100
1.8-1.840.2162180.19044095X-RAY DIFFRACTION100
1.84-1.870.20862330.16984075X-RAY DIFFRACTION100
1.87-1.910.19562120.1674110X-RAY DIFFRACTION100
1.91-1.950.19871980.16744080X-RAY DIFFRACTION100
1.95-20.20222250.17254071X-RAY DIFFRACTION100
2-2.050.21092460.17024059X-RAY DIFFRACTION100
2.05-2.10.20362270.17924090X-RAY DIFFRACTION100
2.1-2.170.22160.15994099X-RAY DIFFRACTION100
2.17-2.240.15621920.14764107X-RAY DIFFRACTION100
2.24-2.320.17542210.14564092X-RAY DIFFRACTION100
2.32-2.410.19022050.15434142X-RAY DIFFRACTION100
2.41-2.520.19832270.15314119X-RAY DIFFRACTION100
2.52-2.650.18072100.1554152X-RAY DIFFRACTION100
2.65-2.820.19122030.15464148X-RAY DIFFRACTION100
2.82-3.030.16932390.16074125X-RAY DIFFRACTION100
3.03-3.340.18662290.15164162X-RAY DIFFRACTION100
3.34-3.820.19122190.14894193X-RAY DIFFRACTION100
3.82-4.810.14312170.13334268X-RAY DIFFRACTION100
4.81-49.170.20352270.19044439X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2109-0.37760.54443.0788-0.19513.98870.0432-0.0193-0.3023-0.0117-0.0436-0.10110.10810.1217-0.00890.15230.0111-0.00620.09590.01970.1745-47.09238.443-24.0267
24.97673.02790.58765.4327-0.20192.9979-0.03310.16690.22140.0025-0.0695-0.2918-0.17380.34290.06510.09090.0159-0.00490.16980.01760.159-42.406422.5932-30.4314
31.40170.58250.05270.55340.15012.9365-0.0256-0.06240.09020.0862-0.0097-0.0021-0.09020.12540.03210.13950.0253-0.01790.10460.02430.1374-49.968326.4719-19.9685
43.90290.9758-0.02275.0849-0.93635.14870.0208-0.11920.5363-0.0962-0.1192-0.1341-0.54620.62580.08650.2156-0.06910.03440.25250.01080.3176-39.926835.0404-10.5371
54.3075-0.74252.96843.2043-2.35945.67150.0035-0.4431-0.1347-0.04130.02640.05660.13640.0001-0.03190.16130.02920.02710.20010.01180.1289-47.437423.5469-6.2838
65.4419-0.0075-1.97131.94291.36976.0379-0.15270.4429-0.2098-0.07720.03520.18920.0423-0.26430.09770.13550.028-0.03250.09680.03370.1504-59.332218.968-29.1752
77.3684-1.01936.63293.3314-1.7047.63190.1869-0.712-0.25140.3747-0.02960.11150.2939-0.4583-0.19350.32990.02310.06280.27560.08230.244-55.867211.5989-9.7461
82.18450.4449-0.26322.45930.00052.2136-0.03710.04930.0345-0.07550.01210.2983-0.0427-0.28750.01460.11650.012-0.01120.1444-0.00570.1331-77.837537.5476-27.2767
91.43420.6864-0.92651.1929-0.43221.7994-0.0275-0.0574-0.10620.0674-0.08730.02510.0832-0.16350.11020.1408-0.0048-0.01310.1484-0.01770.154-75.50825.5119-13.1964
102.202-0.0127-0.51442.4467-0.15572.1610.10350.094-0.0863-0.08730.01380.11150.1018-0.3365-0.03050.1025-0.01120.0110.16450.00090.1233-76.37873.1787-35.5454
112.84150.3989-0.59212.9508-0.79182.2759-0.0480.0409-0.07770.01050.10620.38090.119-0.3566-0.0450.10020.00470.00430.2144-0.00110.159-81.501376.8094-33.0909
122.7862-1.50660.21986.4504-0.9323.7156-0.04150.0823-0.286-0.05140.0326-0.18310.41070.0639-0.00710.1233-0.0426-0.00210.1092-0.0280.1149-68.302465.5098-40.404
130.1845-0.1880.23290.8287-0.40982.3643-0.00550.0194-0.0005-0.0032-0.0184-0.06490.0774-0.0220.02310.1113-0.01720.01320.1409-0.00380.1457-61.726771.055-30.1864
144.634-0.7489-0.81863.2299-1.54277.5306-0.0950.083-0.1229-0.1796-0.1191-0.56280.34660.11130.16420.16370.00090.0430.048-0.03220.26-54.178460.5142-21.5447
153.79711.54810.83395.58540.5452.9478-0.0363-0.0231-0.1144-0.158-0.0164-0.63310.20710.06060.05270.16570.010.05180.1133-0.01950.2023-55.672955.5047-22.2869
167.2875-1.7383.94041.8682-0.82657.69270.0334-0.2852-0.51530.1441-0.08030.24380.5607-0.4408-0.01850.2143-0.0540.05210.1229-0.03830.2294-68.708758.3019-14.1172
177.3211-2.4197-1.61186.4962-4.60575.44630.0620.08150.1219-0.01290.068-0.02810.0301-0.1808-0.12660.109-0.0352-0.02980.1142-0.02730.0641-65.946568.8519-18.1406
187.25783.6445-6.02291.94-3.04167.02150.1742-0.09280.17520.2579-0.12380.0945-0.2088-0.0863-0.03670.17270.00080.00950.1036-0.02220.1525-64.507370.3971-13.9222
192.37890.12681.47374.82391.40493.9401-0.02030.15330.1644-0.4578-0.0913-0.0037-0.1840.08030.10140.0767-0.01320.02740.13210.01950.1025-64.675582.1314-39.3886
204.79163.6622-4.14756.2607-4.89384.40660.0617-0.33340.06780.74190.03950.1282-0.4403-0.0038-0.09850.23460.02620.01740.2553-0.05120.207-73.011382.29-19.766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 187 )
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 217 )
6X-RAY DIFFRACTION6chain 'A' and (resid 218 through 243 )
7X-RAY DIFFRACTION7chain 'A' and (resid 244 through 264 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 93 )
9X-RAY DIFFRACTION9chain 'B' and (resid 94 through 264 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 20 )
11X-RAY DIFFRACTION11chain 'C' and (resid 21 through 47 )
12X-RAY DIFFRACTION12chain 'C' and (resid 48 through 79 )
13X-RAY DIFFRACTION13chain 'C' and (resid 80 through 123 )
14X-RAY DIFFRACTION14chain 'C' and (resid 124 through 152 )
15X-RAY DIFFRACTION15chain 'C' and (resid 153 through 173 )
16X-RAY DIFFRACTION16chain 'C' and (resid 174 through 187 )
17X-RAY DIFFRACTION17chain 'C' and (resid 188 through 202 )
18X-RAY DIFFRACTION18chain 'C' and (resid 203 through 217 )
19X-RAY DIFFRACTION19chain 'C' and (resid 218 through 243 )
20X-RAY DIFFRACTION20chain 'C' and (resid 244 through 264 )

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