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- PDB-6yk2: Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2... -

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Basic information

Entry
Database: PDB / ID: 6yk2
TitleStructure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound (S)-1-[2'-Amino-2'-carboxyethyl]-5,7-dihydrothieno[3,4-d]pyrimidin- 2,4(1H,3H)-dione at resolution 1.60A
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 / 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 / extracellularly glutamate-gated ion channel activity ...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 / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / 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 / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic transmission, glutamatergic / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / 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 / Periplasmic binding protein-like I
Similarity search - Domain/homology
Chem-CGW / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.612 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,32011
Polymers29,2791
Non-polymers1,04110
Water6,161342
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)60,64022
Polymers58,5572
Non-polymers2,08320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4820 Å2
ΔGint-91 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.274, 96.530, 48.711
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-570-

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 , 5 types, 352 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CGW / (2~{S})-2-azanyl-3-[2,4-bis(oxidanylidene)-5,7-dihydrothieno[3,4-d]pyrimidin-1-yl]propanoic acid


Mass: 257.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N3O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 15% PEG4000, 0.3M Lithium Sulfate, 0.1M acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0727 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0727 Å / Relative weight: 1
ReflectionResolution: 1.612→37.424 Å / Num. obs: 35934 / % possible obs: 95.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 11.76 Å2 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.046 / Rsym value: 0.038 / Net I/av σ(I): 12.5 / Net I/σ(I): 18.6 / Num. measured all: 99021
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allRsym value% possible all
1.612-1.692.50.1074.941640.1340.10777.2
1.69-1.792.70.0836.451280.1040.083100
1.79-1.912.70.0637.848120.0780.063100
1.91-2.072.80.057.745050.0620.0599.9
2.07-2.262.80.04510.941540.0550.04599.8
2.26-2.532.90.0371537510.0450.03799.6
2.53-2.922.90.03218.433330.0390.03299.2
2.92-3.582.90.0319.927940.0360.0398.6
3.58-5.062.70.02821.921330.0350.02895.4
5.06-37.4242.70.02921.211600.0360.02990

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Processing

Software
NameVersionClassification
SCALA3.2.5data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SYH

1syh


Resolution: 1.612→35.063 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.31
RfactorNum. reflection% reflection
Rfree0.1628 1794 5 %
Rwork0.1452 --
obs0.1461 35875 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.27 Å2 / Biso mean: 15.2915 Å2 / Biso min: 4.89 Å2
Refinement stepCycle: final / Resolution: 1.612→35.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 63 346 2394
Biso mean--31.65 25.65 -
Num. residues----262
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.612-1.65510.17631010.1613215181
1.6551-1.70380.1921330.15672658100
1.7038-1.75880.16561330.16482671100
1.7588-1.82170.20331350.1552663100
1.8217-1.89460.17831280.15152649100
1.8946-1.98080.1781370.14522660100
1.9808-2.08520.16441610.13572636100
2.0852-2.21580.14911260.13382694100
2.2158-2.38690.14861440.1343266399
2.3869-2.6270.16711470.1372267599
2.627-3.0070.16421500.1453267299
3.007-3.78780.14521570.1345266698
3.7878-35.0630.16581420.1627262391
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)
10.3231-0.1034-0.05860.23110.10610.2529-0.0067-0.013-0.01910.00340.00350.0573-0.0274-0.01590.00290.05910.001900.05230.00210.058311.60919.161332.5724
20.18260.03850.04730.2506-0.02890.2406-0.03470.00820.0143-0.02790.0135-0.0219-0.0093-0.0011-00.0502-0.0074-0.00330.0595-0.00480.053225.538616.409717.4456
30.26250.115-0.04050.1741-0.09240.0418-0.03440.0277-0.036-0.03680.0550.0026-0.01450.0446-0.00040.0678-0.0013-0.00560.0612-0.00450.080118.2477-1.211926.1197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )A1 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 217 )A80 - 217
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 262 )A218 - 262

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