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- PDB-4lz7: Crystal structures of GLuR2 ligand-binding-domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 4lz7
TitleCrystal structures of GLuR2 ligand-binding-domain in complex with glutamate and positive allosteric modulators
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / AMPA receptor / allosteric modulator
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 / immunoglobulin binding ...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 / 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 / positive regulation of synaptic transmission / glutamate receptor binding / 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 / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor 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 / Schaffer collateral - CA1 synapse / terminal bouton / 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
Chem-1YW / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPandit, J.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Discovery and Characterization of a Novel Dihydroisoxazole Class of alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) Receptor Potentiators.
Authors: Patel, N.C. / Schwarz, J. / Hou, X.J. / Hoover, D.J. / Xie, L. / Fliri, A.J. / Gallaschun, R.J. / Lazzaro, J.T. / Bryce, D.K. / Hoffmann, W.E. / Hanks, A.N. / McGinnis, D. / Marr, E.S. / ...Authors: Patel, N.C. / Schwarz, J. / Hou, X.J. / Hoover, D.J. / Xie, L. / Fliri, A.J. / Gallaschun, R.J. / Lazzaro, J.T. / Bryce, D.K. / Hoffmann, W.E. / Hanks, A.N. / McGinnis, D. / Marr, E.S. / Gazard, J.L. / Hajos, M. / Scialis, R.J. / Hurst, R.S. / Shaffer, C.L. / Pandit, J. / O'Donnell, C.J.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,41113
Polymers91,0323
Non-polymers1,37910
Water4,522251
1
A: Glutamate receptor 2
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4848
Polymers60,6882
Non-polymers7966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-41 kcal/mol
Surface area22930 Å2
MethodPISA
2
B: Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,85410
Polymers60,6882
Non-polymers1,1678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2330 Å2
ΔGint-87 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.380, 164.344, 47.402
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRMETMET2AA394 - 40817 - 31
21THRTHRMETMET2BB394 - 40817 - 31
31THRTHRMETMET2CC394 - 40817 - 31
12ARGARGALAALA2AA420 - 67743 - 177
22ARGARGALAALA2BB420 - 67743 - 177
32ARGARGALAALA2CC420 - 67743 - 177
13VALVALCYSCYS2AA681 - 773181 - 273
23VALVALCYSCYS2BB681 - 773181 - 273
33VALVALCYSCYS2CC681 - 773181 - 273
14GLUGLUGLUGLU1AE802
24GLUGLUGLUGLU1BH803
34GLUGLUGLUGLU1CL803

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Components

#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 / AMPA receptor


Mass: 30343.840 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999 / Mutation: G389R,L390G,E391A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19491
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-1YW / N-({(5S)-3-[3-fluoro-4-(pyrrolidin-1-yl)phenyl]-4,5-dihydro-1,2-oxazol-5-yl}methyl)acetamide


Mass: 305.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20FN3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPROTEIN CONSTRUCT COMPRISES UNP RESIDUES 404-527 AND UNP RESIDUES 653-796 CONNECTED BY A GT LINKER.

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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: 49.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1 uL 7 mg/mL protein in 10 mM (S)-Glu, 10 mM HEPES, pH 7.5, 20 mM sodium chloride, 1 mM EDTA, 150 uM ligand (from 30 mM DMSO stock) + 1 uL reservoir (10% PEG8000, 0.1 M zinc acetate, 0.1 M ...Details: 1 uL 7 mg/mL protein in 10 mM (S)-Glu, 10 mM HEPES, pH 7.5, 20 mM sodium chloride, 1 mM EDTA, 150 uM ligand (from 30 mM DMSO stock) + 1 uL reservoir (10% PEG8000, 0.1 M zinc acetate, 0.1 M sodium acetate, pH 5.5), crystals appeared in 3-5 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 53393 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.142 / Χ2: 1.153 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.187.10.71952811.1381100
2.18-2.267.10.58652641.2261100
2.26-2.377.20.50752491.2071100
2.37-2.497.20.43352901.221100
2.49-2.657.20.32852771.2221100
2.65-2.857.30.24652701.2571100
2.85-3.147.30.16653311.2051100
3.14-3.597.30.10353601.151100
3.59-4.527.20.06954061.0211100
4.52-306.90.05556650.896199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LBC

1lbc


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2278 / WRfactor Rwork: 0.1863 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8358 / SU B: 9.225 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2158 / SU Rfree: 0.1869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 2674 5 %RANDOM
Rwork0.1955 ---
obs0.1978 53166 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.42 Å2 / Biso mean: 17.1859 Å2 / Biso min: 1.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6035 0 79 251 6365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226242
X-RAY DIFFRACTIONr_bond_other_d0.0010.024351
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9868388
X-RAY DIFFRACTIONr_angle_other_deg1.0043.00110641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3725766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84824.39246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.814151177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4241530
X-RAY DIFFRACTIONr_chiral_restr0.0930.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021216
X-RAY DIFFRACTIONr_nbd_refined0.2460.21195
X-RAY DIFFRACTIONr_nbd_other0.20.24269
X-RAY DIFFRACTIONr_nbtor_refined0.180.23007
X-RAY DIFFRACTIONr_nbtor_other0.090.23177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2294
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.28
X-RAY DIFFRACTIONr_mcbond_it1.0131.54002
X-RAY DIFFRACTIONr_mcbond_other0.2481.51593
X-RAY DIFFRACTIONr_mcangle_it1.38726129
X-RAY DIFFRACTIONr_scbond_it2.28132704
X-RAY DIFFRACTIONr_scangle_it3.3854.52259
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1215TIGHT POSITIONAL0.140.05
B1215TIGHT POSITIONAL0.110
C1215TIGHT POSITIONAL0.160
A1536MEDIUM POSITIONAL0.370.5
B1536MEDIUM POSITIONAL0.350
C1536MEDIUM POSITIONAL0.320
A1215TIGHT THERMAL0.620.5
B1215TIGHT THERMAL0.630
C1215TIGHT THERMAL0.720
A1536MEDIUM THERMAL0.722
B1536MEDIUM THERMAL0.80
C1536MEDIUM THERMAL0.820
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 190 -
Rwork0.241 3718 -
all-3908 -
obs--100 %

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