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- PDB-1p1w: Crystal structure of the GluR2 ligand-binding core (S1S2J) with t... -

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Basic information

Entry
Database: PDB / ID: 1p1w
TitleCrystal structure of the GluR2 ligand-binding core (S1S2J) with the L483Y and L650T mutations and in complex with AMPA
ComponentsGlutamate receptor 2 precursor
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor / AMPA receptor / ion channel
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / synapse / glutamatergic synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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-AMQ / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArmstrong, N. / Mayer, M.L. / Gouaux, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Tuning activation of the AMPA-sensitive GluR2 ion channel by genetic adjustment of agonist-induced conformational changes.
Authors: Armstrong, N. / Mayer, M. / Gouaux, E.
History
DepositionApr 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 27, 2021Group: 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). NOTE THAT COORDINATES FOR ONE DIMER OF A COMPLETE TETRAMERIC MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN IN REMARK 350. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
Remark 999SEQUENCE The native GLUR-2 is a membrane protein. The protein crystallized by the author is the ...SEQUENCE The native GLUR-2 is a membrane protein. The protein crystallized by the author is the extracellular ligand binding domain of GLUR-2. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker. The sequence, as a result, matches discontinuously with the reference database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,0846
Polymers58,5192
Non-polymers5644
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.883, 121.471, 47.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 29259.646 Da / Num. of mol.: 2 / Fragment: ligand binding core (S1S2J) / Mutation: L94Y,L138T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIA2 OR GLUR2 / Plasmid: pETGQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P19491
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMQ / (S)-ALPHA-AMINO-3-HYDROXY-5-METHYL-4-ISOXAZOLEPROPIONIC ACID / AMPA / AMPA


Mass: 186.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10N2O4 / Comment: neurotransmitter, agonist*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG4000, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMAMPA1reservoir
214-18 %PEG40001reservoir
30.2-0.4 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.973 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 52581 / Num. obs: 51658 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.07 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.88 Å / Rmerge(I) obs: 0.283 / % possible all: 90.7
Reflection
*PLUS
Num. obs: 52581
Reflection shell
*PLUS
% possible obs: 90.7 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.98 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3643 7.1 %RANDOM
Rwork0.234 ---
all0.234 51645 --
obs0.234 51645 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.6179 Å2 / ksol: 0.385286 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.17 Å20 Å20 Å2
2---3.01 Å20 Å2
3----3.17 Å2
Refine analyzeLuzzati coordinate error free: 0.28 Å / Luzzati sigma a free: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 36 235 4143
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 541 6.7 %
Rwork0.27 7547 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2AMPA.PARAMPA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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