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- PDB-3tza: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in c... -

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Basic information

Entry
Database: PDB / ID: 3tza
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the antagonist (S)-2-amino-3-(2-(2-carboxyethyl)-5-chloro-4-nitrophenyl)propionic acid at 1.9A resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor ligand-binding domain / GluA2-S1S2J / antagonist
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 / cellular response to glycine / AMPA glutamate receptor complex / 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 / cellular response to brain-derived neurotrophic factor stimulus / extracellular ligand-gated monoatomic ion channel activity / 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 / signaling receptor activity / presynapse / amyloid-beta binding / growth cone / presynaptic membrane / scaffold protein binding / perikaryon / dendritic spine / chemical synaptic transmission / 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
Chem-TZG / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFrydenvang, K. / Kastrup, J.S.
CitationJournal: J.Med.Chem. / Year: 2011
Title: A new phenylalanine derivative acts as an antagonist at the AMPA receptor GluA2 and introduces partial domain closure: synthesis, resolution, pharmacology, and crystal structure
Authors: Szymanska, E. / Frydenvang, K. / Contreras-Sanz, A. / Pickering, D.S. / Frola, E. / Serafimoska, Z. / Nielsen, B. / Kastrup, J.S. / Johansen, T.N.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _struct.pdbx_descriptor / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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
A: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4618
Polymers58,4432
Non-polymers1,0186
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-52 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.722, 61.835, 92.921
Angle α, β, γ (deg.)90.000, 94.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: 29221.682 Da / Num. of mol.: 2
Fragment: Ligand binding domain, UNP resiudes 413-527,UNP residues 653-796
Source method: isolated from a genetically manipulated source
Details: The protein crystallized is the extracellular ligand-binding domian of GluA2. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker.
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
#2: Chemical ChemComp-TZG / (S)-2-amino-3-(2-(2-carboxyethyl)-5-chloro-4-nitrophenyl)propionic acid


Mass: 316.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13ClN2O6
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15.2% PEG4000, 0.1M ammonium sulfate, 0.1M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→92.848 Å / Num. all: 41312 / Num. obs: 41312 / % possible obs: 94.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-23.50.2980.2532.91730349780.1570.2980.2533.978.6
2-2.123.80.2020.1734.12201058300.1030.2020.1736.797.2
2.12-2.273.70.1830.1564.42033454420.0940.1830.1569.997.4
2.27-2.453.80.120.1036.91938151370.0610.120.10312.697.6
2.45-2.693.80.0870.0749.21781347190.0440.0870.07416.898
2.69-33.80.0660.05611.51610542840.0340.0660.05622.898
3-3.473.70.0510.04314.51425238040.0260.0510.04328.598.3
3.47-4.253.70.0420.03617.31198932230.0210.0420.03632.398.5
4.25-6.013.70.0390.03317.9926325200.020.0390.03334.698.4
6.01-46.3243.50.0470.03910.3475313750.0260.0470.03935.196.4

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N0T

1n0t


Resolution: 1.9→38.209 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8273 / SU ML: 0.27 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 2077 5.03 %RANDOM
Rwork0.1715 ---
obs0.1745 41297 94.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.678 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 138.35 Å2 / Biso mean: 26.9196 Å2 / Biso min: 6.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.2065 Å2-0 Å23.0636 Å2
2---4.1782 Å2-0 Å2
3---2.9717 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 62 632 4747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054234
X-RAY DIFFRACTIONf_angle_d0.9495703
X-RAY DIFFRACTIONf_chiral_restr0.067621
X-RAY DIFFRACTIONf_plane_restr0.004716
X-RAY DIFFRACTIONf_dihedral_angle_d15.5761569
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.94420.2941860.216419532039195370
1.9442-1.99280.24621190.199922982417229883
1.9928-2.04670.29041350.189826282763262896
2.0467-2.10690.25421430.19526822825268297
2.1069-2.17490.321330.225926652798266597
2.1749-2.25260.28291560.212126502806265097
2.2526-2.34280.26451530.183426502803265097
2.3428-2.44940.26121390.175827192858271997
2.4494-2.57850.24561400.173526732813267398
2.5785-2.74010.24371370.171626942831269498
2.7401-2.95150.23451310.176727042835270498
2.9515-3.24840.2371440.16227432887274398
3.2484-3.71810.21651590.147426872846268798
3.7181-4.68310.16861470.122127192866271998
4.6831-38.21720.15571550.143827552910275597

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