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- PDB-3o6h: Ligand-binding domain of GluA2 (flip) ionotropic glutamate recept... -

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Basic information

Entry
Database: PDB / ID: 3o6h
TitleLigand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / Membrane Protein / Fusion protein / chimera 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 / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / extracellularly glutamate-gated ion channel activity ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / 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 / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic transmission, glutamatergic / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / terminal bouton / Schaffer collateral - CA1 synapse / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / 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-O25 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMaclean, J.K.F. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Jamieson, C. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. ...Maclean, J.K.F. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Jamieson, C. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Martin, F. / Moir, E.M. / Morrow, J.A. / Pantling, J. / Rankovic, Z. / Smith, L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: A novel series of positive modulators of the AMPA receptor: structure-based lead optimization.
Authors: Jamieson, C. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Maclean, J.K. / Martin, F. / Moir, E.M. / Morrow, J.A. / ...Authors: Jamieson, C. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Maclean, J.K. / Martin, F. / Moir, E.M. / Morrow, J.A. / Pantling, J. / Rankovic, Z. / Smith, L.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2459
Polymers29,1781
Non-polymers1,0678
Water1,44180
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,48918
Polymers58,3552
Non-polymers2,13416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)63.890, 87.450, 47.320
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, 1 molecules A

#1: Protein Glutamate receptor 2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / AMPA-selective ...GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / AMPA-selective glutamate receptor 2


Mass: 29177.670 Da / Num. of mol.: 1
Fragment: Ligand binding domain, UNP residues 413 to 527 and 653 to 796
Source method: isolated from a genetically manipulated source
Details: S1-S2 fusion in which Gly118 and Thr119 replace a membrane-spanning region
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P19491

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Non-polymers , 6 types, 88 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-O25 / 2-[({4-[(ethylamino)methyl]-3-(trifluoromethyl)-1H-pyrazol-1-yl}acetyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide


Mass: 429.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22F3N5O2S
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 18% PEG 4000, 100mM Sodium Cacodylate pH 4.0, 50mM Lithium Sulphate, 5% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 8, 2006
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→43.73 Å / Num. all: 15217 / Num. obs: 15217 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.17 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.28 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 4 / Num. unique all: 1441 / % possible all: 91.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.73 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.587 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26295 750 4.9 %RANDOM
Rwork0.21714 ---
all0.21943 14467 --
obs0.21943 14467 94.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2--1.69 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 66 80 2179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222224
X-RAY DIFFRACTIONr_bond_other_d0.0060.021542
X-RAY DIFFRACTIONr_angle_refined_deg1.3662.0033004
X-RAY DIFFRACTIONr_angle_other_deg1.1673.0013786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.855278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65124.28684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74815421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1691511
X-RAY DIFFRACTIONr_chiral_restr0.1140.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022435
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_nbd_refined0.1960.2420
X-RAY DIFFRACTIONr_nbd_other0.1910.21515
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21063
X-RAY DIFFRACTIONr_nbtor_other0.0860.21103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.210
X-RAY DIFFRACTIONr_mcbond_it1.3331.51753
X-RAY DIFFRACTIONr_mcbond_other0.151.5557
X-RAY DIFFRACTIONr_mcangle_it1.20122188
X-RAY DIFFRACTIONr_scbond_it2.23331055
X-RAY DIFFRACTIONr_scangle_it2.9554.5816
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 44 -
Rwork0.244 1023 -
obs--90.04 %

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