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- PDB-4iy5: Crystal structure of the glua2 ligand-binding domain (S1S2J-L483Y... -

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Basic information

Entry
Database: PDB / ID: 4iy5
TitleCrystal structure of the glua2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and CX516 at 2.0 A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor ligand-binding domain / GLUA2 S1S2J-L483Y-N754S / CX516 / 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 / 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
piperidin-1-yl(quinoxalin-6-yl)methanone / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKrintel, C. / Frydenvang, K. / Harpsoe, K. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural analysis of the positive AMPA receptor modulators CX516 and Me-CX516 in complex with the GluA2 ligand-binding domain
Authors: Krintel, C. / Harpsoe, K. / Zachariassen, L.G. / Peters, D. / Frydenvang, K. / Pickering, D.S. / Gajhede, M. / Kastrup, J.S.
#1: 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.
#2: Journal: J.Neurosci. / Year: 2005
Title: Mechanism of positive allosteric modulators acting on AMPA receptors.
Authors: Jin, R. / Clark, S. / Weeks, A.M. / Dudman, J.T. / Gouaux, E. / Partin, K.M.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 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 1.3Nov 20, 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)59,88816
Polymers58,4892
Non-polymers1,39914
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-82 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.080, 121.690, 47.300
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, 2 molecules AB

#1: Protein 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: 29244.678 Da / Num. of mol.: 2
Fragment: Ligand binding domain, UNP RESIDUES 413-527, 653-796
Mutation: L94Y, N242S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur2, Gria2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: P19491

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Non-polymers , 6 types, 586 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-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CX5 / piperidin-1-yl(quinoxalin-6-yl)methanone


Mass: 241.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N3O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE FUSION PROTEIN OF THE RESIDUES 413-527, LINKER GLY-THR, AND RESIDUES 653-796 FROM GLUA2

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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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 24.4% PEG 4000, 0.3M lithium sulfate, 0.1M phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03796 Å / Relative weight: 1
ReflectionResolution: 2→26.432 Å / Num. obs: 39394 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2-2.115.20.3134.556871100
2.11-2.245.20.216654011100
2.24-2.395.20.1937.150611100
2.39-2.585.20.1578.147321100
2.58-2.835.20.12510.143761100
2.83-3.165.20.09412.53985199.3
3.16-3.655.20.07416.13530199.9
3.65-4.475.20.05718.82972199.5
4.47-6.325.10.06617.82334198.9
6.32-26.434.90.06517.71316195.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TDJ

3tdj


Resolution: 2→26.432 Å / SU ML: 0.18 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1974 5.02 %Random
Rwork0.153 ---
obs0.1553 39351 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.2 Å2
Refinement stepCycle: LAST / Resolution: 2→26.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 84 572 4751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074333
X-RAY DIFFRACTIONf_angle_d1.0385840
X-RAY DIFFRACTIONf_dihedral_angle_d13.0091660
X-RAY DIFFRACTIONf_chiral_restr0.071635
X-RAY DIFFRACTIONf_plane_restr0.004726
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2-2.050.24571430.18626512651100
2.05-2.10540.24371470.170526212621100
2.1054-2.16740.21931560.157626082608100
2.1674-2.23730.22751550.154626432643100
2.2373-2.31720.21861230.157426422642100
2.3172-2.40990.22621420.153326552655100
2.4099-2.51950.19781290.161726652665100
2.5195-2.65220.24821360.164126692669100
2.6522-2.81820.22681410.16626762676100
2.8182-3.03550.21961490.170126582658100
3.0355-3.34050.19671490.152826902690100
3.3405-3.82260.16011260.136727012701100
3.8226-4.81140.15091340.11822724272499
4.8114-26.43470.17021440.16162774277496
Refinement TLS params.Method: refined / Origin x: 29.3718 Å / Origin y: 16.8211 Å / Origin z: 3.3744 Å
111213212223313233
T0.0644 Å20.0103 Å2-0.0003 Å2-0.0742 Å2-0.0047 Å2--0.0627 Å2
L0.3325 °20.1887 °20.1157 °2-0.5317 °20.0042 °2--0.3714 °2
S0.0079 Å °0.0149 Å °-0.0126 Å °0.0001 Å °-0.0187 Å °-0.0257 Å °-0.0273 Å °0.0327 Å °0.0121 Å °
Refinement TLS groupSelection details: ALL

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