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- PDB-2p2a: X-ray structure of the GluR2 ligand binding core (S1S2J) in compl... -

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Basic information

Entry
Database: PDB / ID: 2p2a
TitleX-ray structure of the GluR2 ligand binding core (S1S2J) in complex with 2-Bn-tet-AMPA at 2.26A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor GluR2 / ligand-binding core / agonist complex
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 / ionotropic glutamate receptor binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / somatodendritic compartment / glutamate-gated calcium ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / 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 / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / 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-MP9 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsFrydenvang, K. / Kastrup, J.S. / Gajhede, M.
Citation
Journal: J.Med.Chem. / Year: 2007
Title: A tetrazolyl-substituted subtype-selective AMPA receptor agonist.
Authors: Vogensen, S.B. / Frydenvang, K. / Greenwood, J.R. / Postorino, G. / Nielsen, B. / Pickering, D.S. / Ebert, B. / Bolcho, U. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. / Johansen, T.N. / ...Authors: Vogensen, S.B. / Frydenvang, K. / Greenwood, J.R. / Postorino, G. / Nielsen, B. / Pickering, D.S. / Ebert, B. / Bolcho, U. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. / Johansen, T.N. / Clausen, R.P. / Krogsgaard-Larsen, P.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Structural Basis for AMPA Receptor Activation and Ligand Selectivity: Crystal Structures of Five Agonist Complexes with the GluR2 ligand-binding core
Authors: Hogner, A. / Kastrup, J.S. / Jin, R. / Liljefors, T. / Mayer, M.L. / Egebjerg, J. / Larsen, I.K. / Gouaux, E.
#2: Journal: Neuron / Year: 2000
Title: Mechanisms for Activation and Antagonism of an AMPA-sensitive Glutamate Receptor: Crystal Structures of the GluR2 ligand binding core
Authors: Armstrong, N. / Gouaux, E.
#3: Journal: FEBS Lett. / Year: 2002
Title: GluR2 Ligand-Binding Core Complexes: Importance of the Isoxazolol Moiety and 5-Substituent for the Binding Mode of AMPA-type Agonists.
Authors: Kasper, C. / Lunn, M.L. / Liljefors, T. / Gouaux, E. / Egebjerg, J. / Kastrup, J.S.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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_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 20, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,2097
Polymers58,4432
Non-polymers7665
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-60 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.120, 121.980, 47.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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: 29221.682 Da / Num. of mol.: 2
Fragment: GluR2-Flop ligand-binding core (Residues 413-527, 653-796)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2 / Plasmid: PET30B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19491
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-MP9 / 2-AMINO-3-[3-HYDROXY-5-(2-BENZYL-2H-5-TETRAZOLYL)-4-ISOXAZOLYL]-PROPIONIC ACID / 3-[5-(2-BENZYL-2H-TETRAZOL-5-YL)-3-HYDROXYISOXAZOL-4-YL]-L-ALANINE / 2-BN-TET-AMPA


Mass: 330.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000, Sodium Acetate, Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0628 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0628 Å / Relative weight: 1
ReflectionResolution: 2.26→25 Å / Num. all: 27218 / Num. obs: 27218 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 16.1
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 7.7 / Num. unique all: 3895 / Rsym value: 0.18 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NNP

1nnp


Resolution: 2.26→25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1797506.97 / Data cutoff low absF: 0 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Chain A: residues -2, -1, 255, 259, and 260 were not located in electron density map. Chain B: residues -2, -1, 0, 254, 255, 256, 259, and 260 were not located in electron density map.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1362 5 %Random
Rwork0.211 ---
all-27158 --
obs-27158 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4311 Å2 / ksol: 0.403563 e/Å3
Displacement parametersBiso mean: 19.348 Å2
Baniso -1Baniso -2Baniso -3
1--7.883 Å20 Å20 Å2
2--3.235 Å20 Å2
3---4.648 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.26→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 49 410 4473
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061.5
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_dihedral_angle_d21.72
X-RAY DIFFRACTIONc_improper_angle_d0.742.5
X-RAY DIFFRACTIONc_mcbond_it1.4321.5
X-RAY DIFFRACTIONc_mcangle_it2.1782
X-RAY DIFFRACTIONc_scbond_it2.2212
X-RAY DIFFRACTIONc_scangle_it3.1332.5
LS refinement shellResolution: 2.26→2.4 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 247 5.6 %
Rwork0.258 4183 -
obs-4183 99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water_rep.top
X-RAY DIFFRACTION32benztet.par2benztet.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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