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- PDB-5elv: Crystal structure of the GluA2 ligand-binding domain (S1S2J-L504-... -

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Basic information

Entry
Database: PDB / ID: 5elv
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J-L504-N775) in complex with glutamate and BPAM-521 at 1.92 A resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA RECEPTOR LIGAND-BINDING DOMAIN / BPAM-521 ALLOSTERIC MODULATION / FUSION PROTEIN
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / 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 / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / 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-5PX / ACETATE ION / GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsKrintel, C. / Juknaite, L. / Frydenvang, K. / Kastrup, J.S.
Citation
Journal: Biophys.J. / Year: 2016
Title: Enthalpy-Entropy Compensation in the Binding of Modulators at Ionotropic Glutamate Receptor GluA2.
Authors: Krintel, C. / Francotte, P. / Pickering, D.S. / Juknaite, L. / Phlsgaard, J. / Olsen, L. / Frydenvang, K. / Goffin, E. / Pirotte, B. / Kastrup, J.S.
#1: Journal: J. Med. Chem. / Year: 2013
Title: Synthesis, pharmacological and structural characterization, and thermodynamic aspects of GluA2-positive allosteric modulators with a 3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide scaffold.
Authors: Noerholm, A.B. / Francotte, P. / Olsen, L. / Krintel, C. / Frydenvang, K. / Goffin, E. / Challal, S. / Danober, L. / Botez-Pop, I. / Lestage, P. / Pirotte, B. / Kastrup, J.S.
#2: Journal: Biochem. J. / Year: 2012
Title: Thermodynamics and structural analysis of positive allosteric modulation of the ionotropic glutamate receptor GluA2.
Authors: Krintel, C. / Frydenvang, K. / Olsen, L. / Kristensen, M.T. / de Barrios, O. / Naur, P. / Francotte, P. / Pirotte, B. / Gajhede, M. / Kastrup, J.S.
#3: Journal: J. Med. Chem. / Year: 2014
Title: Positive allosteric modulators of 2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic acid receptors belonging to 4-cyclopropyl-3,4-dihydro-2h-1,2,4-pyridothiadiazine dioxides and diversely ...Title: Positive allosteric modulators of 2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic acid receptors belonging to 4-cyclopropyl-3,4-dihydro-2h-1,2,4-pyridothiadiazine dioxides and diversely chloro-substituted 4-cyclopropyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxides.
Authors: Francotte, P. / Noerholm, A.B. / Deva, T. / Olsen, L. / Frydenvang, K. / Goffin, E. / Fraikin, P. / de Tullio, P. / Challal, S. / Thomas, J.Y. / Iop, F. / Louis, C. / Botez-Pop, I. / ...Authors: Francotte, P. / Noerholm, A.B. / Deva, T. / Olsen, L. / Frydenvang, K. / Goffin, E. / Fraikin, P. / de Tullio, P. / Challal, S. / Thomas, J.Y. / Iop, F. / Louis, C. / Botez-Pop, I. / Lestage, P. / Danober, L. / Kastrup, J.S. / Pirotte, B.
#4: Journal: Biochemistry / Year: 2009
Title: Probing the allosteric modulator binding site of GluR2 with thiazide derivatives.
Authors: Ptak, C.P. / Ahmed, A.H. / Oswald, R.E.
History
DepositionNov 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,98128
Polymers58,6032
Non-polymers2,37726
Water7,981443
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-70 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.790, 122.480, 47.540
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,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: 29301.729 Da / Num. of mol.: 2 / Fragment: UNP residues, 413-527,UNP residue, 653-797 / Mutation: L504Y and N775S
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN COMPRISES SEGMENT S1 RESIDUES 413-527, A GT LINKER AND S2 RESIDUES 653-798.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ORIGAMI B / References: UniProt: P19491

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Non-polymers , 8 types, 469 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-5PX / 4-Cyclopropyl-3,4-dihydro-7-hydroxy-2H-1,2,4-benzothiadiazine 1,1-dioxide / BPAM-521


Mass: 240.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O3S
#7: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG4000, 0.3 M lithium sulfate and 0.1 M phosphate-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9753 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 1.92→34.25 Å / Num. all: 44908 / Num. obs: 44908 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 14.19 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.097 / Rsym value: 0.088 / Net I/av σ(I): 5.166 / Net I/σ(I): 13.4 / Num. measured all: 228349
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.92-2.025.10.261.93294964460.1180.266.899.9
2.02-2.155.10.1792.43138961440.0830.1798.799.9
2.15-2.295.10.1372.52941157390.0640.13710.799.9
2.29-2.485.10.1085.92765053980.050.10812.1100
2.48-2.725.10.08772543249530.0410.08713.7100
2.72-3.045.10.0718.52327645440.0340.07115.7100
3.04-3.515.10.0678.32042640080.0320.06718.7100
3.51-4.2950.06781733034350.0320.06721.5100
4.29-6.0750.0598.31343927090.0290.05921.999.9
6.07-31.8014.60.04610.7704715320.0240.04620.797.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TDJ

3tdj


Resolution: 1.92→31.801 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 2265 5.05 %random
Rwork0.1621 42581 --
obs0.1644 44846 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.71 Å2 / Biso mean: 17.8297 Å2 / Biso min: 1.5 Å2
Refinement stepCycle: final / Resolution: 1.92→31.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4096 0 149 444 4689
Biso mean--29.33 25.27 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074485
X-RAY DIFFRACTIONf_angle_d1.0116065
X-RAY DIFFRACTIONf_chiral_restr0.042662
X-RAY DIFFRACTIONf_plane_restr0.004760
X-RAY DIFFRACTIONf_dihedral_angle_d12.6481740
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.96170.23681460.173426362782100
1.9617-2.00740.23311350.1782585272099
2.0074-2.05760.26371340.171926412775100
2.0576-2.11320.23081560.171526232779100
2.1132-2.17540.19881190.161626252744100
2.1754-2.24560.23611340.161626542788100
2.2456-2.32580.21361400.162226212761100
2.3258-2.41890.23371550.164126402795100
2.4189-2.52890.23451350.169226362771100
2.5289-2.66220.1761310.162926612792100
2.6622-2.82890.23561320.167826752807100
2.8289-3.04720.21421390.177626692808100
3.0472-3.35350.20531550.163226742829100
3.3535-3.8380.17721590.148326862845100
3.838-4.83280.16961450.129927302875100
4.8328-31.8050.2211500.182825297599

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