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- PDB-3pmv: Ligand-binding domain of GluA2 (flip) ionotropic glutamate recept... -

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Basic information

Entry
Database: PDB / ID: 3pmv
TitleLigand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / Membrane protein / Fusion protein / chimera protein
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
Chem-557 / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMaclean, J.K.F. / Jamieson, C. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. ...Maclean, J.K.F. / Jamieson, C. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Moir, E.M. / Morrow, J.A. / Pantling, J. / Rankovic, Z. / Smith, L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Structure based evolution of a novel series of positive modulators of the AMPA receptor.
Authors: Jamieson, C. / Maclean, J.K. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Moir, E.M. / Morrow, J.A. / Pantling, J. / ...Authors: Jamieson, C. / Maclean, J.K. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Moir, E.M. / Morrow, J.A. / Pantling, J. / Rankovic, Z. / Smith, L.
History
DepositionNov 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3May 31, 2023Group: 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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,57912
Polymers29,1781
Non-polymers1,40111
Water6,467359
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,15824
Polymers58,3552
Non-polymers2,80322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5280 Å2
ΔGint-135 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.220, 87.230, 47.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate receptor 2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / AMPA-selective ...GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / AMPA-selective glutamate receptor 2


Mass: 29177.670 Da / Num. of mol.: 1
Fragment: Ligand binding domain, residues 413 to 527 and 653 to 796
Source method: isolated from a genetically manipulated source
Details: S1-S2 fusion in which Gly118 and Thr119 replace a membrane-spanning region
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (de3) / References: UniProt: P19491

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Non-polymers , 5 types, 370 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-557 / N-[(2S)-2-{4-[4-(hydroxymethyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl}propyl]propane-2-sulfonamide / (R)-N-(2-(4-(4-(hydroxymethyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl)phenyl)propyl)propane-2-sulfonamide


Mass: 405.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22F3N3O3S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 18% PEG 4000, 50mM Lithium Sulphate, 2.5% Glycerol, 100mM Sodium Cacodylate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 14, 2007 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.79→43.61 Å / Num. all: 24891 / Num. obs: 24891 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2050 / % possible all: 82.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O28

3o28


Resolution: 1.8→43.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.149 / SU ML: 0.099 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25232 1259 5.1 %RANDOM
Rwork0.18394 ---
all0.1987 23631 --
obs0.18716 23631 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--1.04 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 86 359 2488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222307
X-RAY DIFFRACTIONr_bond_other_d0.0010.021601
X-RAY DIFFRACTIONr_angle_refined_deg1.6132.0083118
X-RAY DIFFRACTIONr_angle_other_deg1.3573.0013937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00424.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40415441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6521512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022524
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02444
X-RAY DIFFRACTIONr_nbd_refined0.2050.2448
X-RAY DIFFRACTIONr_nbd_other0.1970.21667
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21061
X-RAY DIFFRACTIONr_nbtor_other0.0890.21118
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.242
X-RAY DIFFRACTIONr_mcbond_it1.72421800
X-RAY DIFFRACTIONr_mcbond_other0.3952570
X-RAY DIFFRACTIONr_mcangle_it1.95332248
X-RAY DIFFRACTIONr_scbond_it3.2134.51099
X-RAY DIFFRACTIONr_scangle_it4.3056869
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 66 -
Rwork0.287 1438 -
obs-1438 80.73 %

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