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- PDB-2aix: X-ray structure of the GLUR2 ligand-binding core (S1S2J) in compl... -

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Basic information

Entry
Database: PDB / ID: 2aix
TitleX-ray structure of the GLUR2 ligand-binding core (S1S2J) in complex with (s)-thio-atpa at 2.2 a 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 / 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 / dendritic spine / chemical synaptic transmission / 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-U1K / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsKastrup, J.S.
Citation
Journal: To be Published
Title: Distinct kinetics of ionotropic glutamate receptor 2 splice variants characterized by fast agonist application and crystallization of a receptor-ligand complex.
Authors: Holm, M.M. / Lunn, M.L. / Traynelis, S.F. / Kastrup, J.S. / Egebjerg, J.
#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. / 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: Nature / Year: 2002
Title: Mechanism of Glutamate Receptor Desensitization.
Authors: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E.
#4: Journal: Protein Sci. / Year: 1998
Title: Probing the Ligand Binding Domain of the Glur2 Receptor by Proteolysis and Deletion Mutagenesis Defines Domain Boundaries and Yields a Crystallizable Construct.
Authors: Chen, G.Q. / Sun, R. / Jin, R. / Gouaux, E.
History
DepositionAug 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE RECEPTOR CONSISTS OF FOUR SUBUNITS CONSTITUTING A TETRAMER. ONE DIMER OF THE TETRAMER CAN BE GENERATED IN THE CRYSTAL. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
Remark 999SEQUENCE Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand- ...SEQUENCE Native GluR2 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 115-116). Therefore, the sequence matches discontinuously with the reference database (413-527, 653-796).

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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)29,4662
Polymers29,2221
Non-polymers2441
Water4,216234
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9324
Polymers58,4432
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Unit cell
Length a, b, c (Å)47.875, 47.875, 240.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 29221.682 Da / Num. of mol.: 1 / Fragment: GLUR2-FLOP LIGAND-BINDING CORE (S1S2J).
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / 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-U1K / (S)-2-AMINO-3-(3-HYDROXY-5-TERT-BUTYLISOTHIAZOL-4-YL) PROPRIONIC ACID / THIO-ATPA


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 48.8 %
Crystal growTemperature: 279 K / pH: 6.5
Details: SODIUM CHLORIDE, CACODYLATE, PEG 8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0835
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0835 Å / Relative weight: 1
ReflectionResolution: 2.17→20 Å / Num. obs: 15624 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.6
Reflection shellResolution: 2.17→2.25 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 7.6 / % possible all: 93.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M5B.

1m5b


Resolution: 2.17→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1987987.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED. / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE FIRST THREE N-TERMINAL RESIDUES AND THE LAST TWO C-TERMINAL RESIDUES WERE NOT LOCATED IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 741 4.8 %RANDOM.
Rwork0.198 ---
obs0.198 15528 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.3512 Å2 / ksol: 0.414103 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.62 Å20 Å20 Å2
2---3.62 Å20 Å2
3---7.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.17→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 16 234 2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.22
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
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_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it3.422.5
LS refinement shellResolution: 2.17→2.31 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.242 111 4.6 %
Rwork0.195 2301 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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