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- PDB-3pd9: X-ray structure of the ligand-binding core of GluA2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3pd9
TitleX-ray structure of the ligand-binding core of GluA2 in complex with (R)-5-HPCA at 2.1 A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor GluA2 / ligand-binding core / agonist complex
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 / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / 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 / dendrite / synapse / 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-HA5 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFrydenvang, K. / Kastrup, J.S.
Citation
Journal: J. Med. Chem. / Year: 2010
Title: Biostructural and pharmacological studies of bicyclic analogues of the 3-isoxazolol glutamate receptor agonist ibotenic acid.
Authors: Frydenvang, K. / Pickering, D.S. / Greenwood, J.R. / Krogsgaard-Larsen, N. / Brehm, L. / Nielsen, B. / Vogensen, S.B. / Hald, H. / Kastrup, J.S. / Krogsgaard-Larsen, P. / Clausen, R.P.
#1: Journal: J.Med.Chem. / Year: 2003
Title: Three-dimensional structure of the ligand-binding core of GluR2 in complex with the agonist (S)-ATPA: implications for receptor subunit selectivity
Authors: Lunn, M.L. / Hogner, A. / Stensbol, T.B. / Gouaux, E. / Egebjerg, J. / Kastrup, J.S.
#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.
History
DepositionOct 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / diffrn_source / entity
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / 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 / _entity.formula_weight / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 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)59,36817
Polymers58,0132
Non-polymers1,35515
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-79 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.391, 121.251, 47.547
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#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: 29006.477 Da / Num. of mol.: 2 / Fragment: UNP residues 413-527, 653-795
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur2, Gria2, RAT / Plasmid: pET30B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19491

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Non-polymers , 5 types, 376 molecules

#2: Chemical ChemComp-HA5 / (5R)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridine-5-carboxylic acid


Mass: 184.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000, ammonium sulfate, acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8126 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 34007 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Χ2: 1.079 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.184.10.41133441.057199.9
2.18-2.264.10.34233351.027199.9
2.26-2.374.10.30133801.0621100
2.37-2.494.10.26433441.1131100
2.49-2.654.10.20433541.143199.9
2.65-2.854.10.15133671.127199.9
2.85-3.144.10.10934111.0871100
3.14-3.594.10.07534091.071100
3.59-4.5240.05634521.045199.9
4.52-303.80.04736111.062199.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
DENZOdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NNP

1nnp


Resolution: 2.1→29.415 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.833 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 1614 5.04 %RANDOM
Rwork0.1769 ---
obs0.1798 32030 93.4 %-
all-32030 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.105 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso max: 97.01 Å2 / Biso mean: 24.953 Å2 / Biso min: 8.31 Å2
Baniso -1Baniso -2Baniso -3
1-5.425 Å2-0 Å2-0 Å2
2---3.438 Å2-0 Å2
3----1.987 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 80 361 4489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074252
X-RAY DIFFRACTIONf_angle_d1.0055725
X-RAY DIFFRACTIONf_chiral_restr0.067626
X-RAY DIFFRACTIONf_plane_restr0.004711
X-RAY DIFFRACTIONf_dihedral_angle_d15.2231580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
2.1-2.16340.24531150.1748X-RAY DIFFRACTION82
2.1634-2.23330.24241160.1721X-RAY DIFFRACTION89
2.2333-2.3130.26351220.1853X-RAY DIFFRACTION92
2.313-2.40560.23981270.183X-RAY DIFFRACTION92
2.4056-2.5150.2681360.1946X-RAY DIFFRACTION91
2.515-2.64760.29931380.197X-RAY DIFFRACTION93
2.6476-2.81330.26511520.1865X-RAY DIFFRACTION94
2.8133-3.03030.24091180.1825X-RAY DIFFRACTION96
3.0303-3.33490.2061420.1649X-RAY DIFFRACTION97
3.3349-3.81660.21991420.1522X-RAY DIFFRACTION99
3.8166-4.80510.18831500.1444X-RAY DIFFRACTION99
4.8051-29.4180.22361560.2006X-RAY DIFFRACTION99

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