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- PDB-3h6w: Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S)... -

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Basic information

Entry
Database: PDB / ID: 3h6w
TitleCrystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS5217 at 1.50 A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor ligand-binding core / iGluR2 S1S2J-N754S / allosteric modulation
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
GLUTAMIC ACID / Chem-NS7 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å
AuthorsHald, H. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Distinct structural features of cyclothiazide are responsible for effects on peak current amplitude and desensitization kinetics at iGluR2.
Authors: Hald, H. / Ahring, P.K. / Timmermann, D.B. / Liljefors, T. / Gajhede, M. / Kastrup, J.S.
#1: 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.
#2: Journal: Nature / Year: 2002
Title: Mechanism of glutamate receptor desensitization.
Authors: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 13, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,90110
Polymers58,3892
Non-polymers1,5128
Water12,304683
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,91510
Polymers58,3892
Non-polymers1,5268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1860 Å2
ΔGint-6.7 kcal/mol
Surface area23610 Å2
MethodPISA
2
B: Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,88710
Polymers58,3892
Non-polymers1,4988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area1760 Å2
ΔGint-7.5 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.010, 47.179, 118.412
Angle α, β, γ (deg.)90.000, 91.880, 90.000
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29194.658 Da / Num. of mol.: 2
Fragment: iGluR2-flop ligand-binding core: UNP residues 413-796
Mutation: N754S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19491

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Non-polymers , 6 types, 691 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-NS7 / (3R)-3-cyclopentyl-6-methyl-7-[(4-methylpiperazin-1-yl)sulfonyl]-3,4-dihydro-2H-1,2-benzothiazine 1,1-dioxide


Mass: 427.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H29N3O4S2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsNATIVE IGLUR2 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING ...NATIVE IGLUR2 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING CORE OF GLUR2. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 118-119). THEREFORE THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (UNP RESIDUES 413-527 AND 653-796, NUMBERING WITH SIGNAL PEPTIDE OF 21 AMINO ACIDS). THE TWO FIRST RESIDUES (GLY, ALA) ARE CLONING REMNANTS.

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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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 % PEG 4000, 0.1 M Ammonium sulfate, 0.1 M Cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.808 Å / Relative weight: 1
ReflectionResolution: 1.49→17.38 Å / Num. obs: 72325 / % possible obs: 85.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 25.2
Reflection shellResolution: 1.49→1.55 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8047 / Rsym value: 0.405 / % possible all: 95.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å17.38 Å
Translation2.5 Å17.38 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FTJ

1ftj


Resolution: 1.49→17.38 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.661 / SU ML: 0.063 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.132 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1392 1.9 %RANDOM
Rwork0.189 ---
obs-71603 84.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.28 Å2 / Biso mean: 19.9 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20.84 Å2
2---1.33 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.49→17.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4081 0 96 683 4860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224373
X-RAY DIFFRACTIONr_bond_other_d0.0020.023035
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9935924
X-RAY DIFFRACTIONr_angle_other_deg0.8723.0047387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65924.529170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57115825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.631520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024765
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02835
X-RAY DIFFRACTIONr_nbd_refined0.2130.2853
X-RAY DIFFRACTIONr_nbd_other0.190.23195
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22182
X-RAY DIFFRACTIONr_nbtor_other0.090.22272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2477
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.240
X-RAY DIFFRACTIONr_mcbond_it1.2021.53458
X-RAY DIFFRACTIONr_mcbond_other0.391.51110
X-RAY DIFFRACTIONr_mcangle_it1.4424304
X-RAY DIFFRACTIONr_scbond_it2.23532054
X-RAY DIFFRACTIONr_scangle_it2.9874.51604
X-RAY DIFFRACTIONr_rigid_bond_restr1.15339158
X-RAY DIFFRACTIONr_sphericity_free4.9373683
X-RAY DIFFRACTIONr_sphericity_bonded2.06537314
LS refinement shellResolution: 1.49→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 121 -
Rwork0.202 5650 -
all-5771 -
obs-5650 92.32 %

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