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- PDB-6yk3: Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2... -

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Basic information

Entry
Database: PDB / ID: 6yk3
TitleStructure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound ( S) - 1- [2'-Amino-2'-carboxyethyl]-5 ,7- dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 1.20A
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / GLUA2O LIGAND-BINDING DOMAIN / BICYCLIC PYRIMIDINEDIONE ANALOGUE
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors ...spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / asymmetric synapse / ionotropic glutamate receptor complex / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / glutamate-gated receptor activity / regulation of long-term synaptic depression / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / dendrite membrane / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / synaptic membrane / dendritic shaft / SNARE binding / 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 / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex 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
AMMONIUM ION / Chem-PVQ / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFrydenvang, K. / Kastrup, J.S.
CitationJournal: Acs Chem Neurosci / Year: 2020
Title: Ionotropic Glutamate Receptor GluA2 in Complex with Bicyclic Pyrimidinedione-Based Compounds: When Small Compound Modifications Have Distinct Effects on Binding Interactions.
Authors: Frydenvang, K. / Pickering, D.S. / Kshirsagar, G.U. / Chemi, G. / Gemma, S. / Sprogoe, D. / Kærn, A.M. / Brogi, S. / Campiani, G. / Butini, S. / Kastrup, J.S.
History
DepositionApr 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)30,36113
Polymers29,2791
Non-polymers1,08212
Water8,809489
1
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)60,72126
Polymers58,5572
Non-polymers2,16424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area5620 Å2
ΔGint-114 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.351, 96.826, 48.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-482-

HOH

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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: 29278.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUA2O. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUE 118-119). THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUA2O. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUE 118-119). THE SEQUENCE MATCHES DISCONTINOUSLY WITH THE REFERENCE DATABASE (UNP RESIDUES 413-527 AND 653-797, NUMBERING WITH SIGNAL PEPTIDE OF 21 AMINO ACIDS). THE TWO FIRST RESIDUES (GLY, ALA) ARE CLONING REMNANTS.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: PET-22B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ORIGAMI B (DE3) / References: UniProt: P19491

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Non-polymers , 6 types, 501 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PVQ / (S)-1-[2'-Amino-2'-carboxyethyl]-5,7-dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione / (2~{S})-2-azanyl-3-[2,4-bis(oxidanylidene)-6,7-dihydro-5~{H}-pyrrolo[3,4-d]pyrimidin-1-yl]propanoic acid


Mass: 240.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20% PEG4000, 0.3M ammonium sulfate, 0.1M acetate

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Data collection

DiffractionMean temperature: 100.5 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→25.318 Å / Num. all: 88027 / Num. obs: 88027 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 7.67 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.079 / Rsym value: 0.07 / Net I/av σ(I): 7.1 / Net I/σ(I): 12.8 / Num. measured all: 421917
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.2-1.264.60.4021.958275127090.210.4560.4023.8100
1.26-1.344.80.2982.557380120730.1530.3360.2984.9100
1.34-1.434.80.223.454152113300.1110.2470.226.5100
1.43-1.554.80.147551080105960.0740.1650.1479.1100
1.55-1.74.90.17.44754197830.050.1120.112.3100
1.7-1.94.90.0749.44318488430.0370.0830.07416100
1.9-2.194.90.05711.13861078830.0280.0630.05721.8100
2.19-2.684.90.0511.83276266770.0250.0560.0525.6100
2.68-3.794.90.04113.42545652120.020.0460.04129.799.6
3.79-25.3014.60.03715.51347729210.0190.0420.03730.597

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALA3.3.9data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SYH

1syh


Resolution: 1.2→23.541 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 10.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1404 4409 5.01 %
Rwork0.1106 83552 -
obs0.1121 87961 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 44.17 Å2 / Biso mean: 12.057 Å2 / Biso min: 3.57 Å2
Refinement stepCycle: final / Resolution: 1.2→23.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 70 501 2577
Biso mean--14.18 24.05 -
Num. residues----263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.21360.19641330.15632795100
1.2136-1.22790.18131390.14332711100
1.2279-1.24290.14041510.13272788100
1.2429-1.25860.17371260.13332770100
1.2586-1.27520.1731270.13452797100
1.2752-1.29270.16521660.1332714100
1.2927-1.31110.17661450.12772759100
1.3111-1.33070.15961360.12072739100
1.3307-1.35150.17581340.1142813100
1.3515-1.37360.14551260.1092770100
1.3736-1.39730.16361440.10052765100
1.3973-1.42270.11961530.09422774100
1.4227-1.45010.1381500.09212754100
1.4501-1.47970.1251490.0882768100
1.4797-1.51180.1111560.08752751100
1.5118-1.5470.12591600.08572730100
1.547-1.58570.11531270.08072802100
1.5857-1.62860.12081390.08022803100
1.6286-1.67650.11231550.082790100
1.6765-1.73060.11241460.08342776100
1.7306-1.79240.11511500.08592783100
1.7924-1.86410.12831560.09112805100
1.8641-1.94890.13061610.09312753100
1.9489-2.05160.10141360.09572816100
2.0516-2.18010.11891530.09672807100
2.1801-2.34830.13141500.10712811100
2.3483-2.58430.16971440.1192849100
2.5843-2.95770.15171500.12472823100
2.9577-3.72390.13541730.1222285399
3.7239-23.5410.17141740.146288396

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