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- PDB-5zg0: Crystal structure of the GluA2o LBD in complex with glutamate and... -

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Basic information

Entry
Database: PDB / ID: 5zg0
TitleCrystal structure of the GluA2o LBD in complex with glutamate and Compound-1
ComponentsGlutamate receptor 2GRIA2
KeywordsTRANSPORT PROTEIN / AMPA RECEPTOR LIGAND-BINDING DOMAIN / ALLOSTERIC MODULATION COMPLEX / MEMBRANE PROTEIN
Function / homology
Function and homology information


Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / excitatory synapse / asymmetric synapse / glutamate-gated receptor activity ...Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / excitatory synapse / asymmetric synapse / glutamate-gated receptor activity / MECP2 regulates neuronal receptors and channels / ionotropic glutamate receptor signaling pathway / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / endocytic vesicle membrane / amyloid-beta binding / postsynapse / chemical synaptic transmission / dendritic spine / postsynaptic density / external side of plasma membrane / neuronal cell body / dendrite / endoplasmic reticulum membrane / signal transduction / 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-9C3 / ACETATE ION / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsSogabe, S. / Igaki, S. / Hirokawa, A. / Zama, Y. / Lane, W. / Snell, G.
CitationJournal: Neuropsychopharmacology / Year: 2019
Title: TAK-137, an AMPA-R potentiator with little agonistic effect, has a wide therapeutic window.
Authors: Kunugi, A. / Tanaka, M. / Suzuki, A. / Tajima, Y. / Suzuki, N. / Suzuki, M. / Nakamura, S. / Kuno, H. / Yokota, A. / Sogabe, S. / Kosugi, Y. / Awasaki, Y. / Kaku, T. / Kimura, H.
History
DepositionMar 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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
D: Glutamate receptor 2
E: Glutamate receptor 2
F: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,06334
Polymers176,0276
Non-polymers3,03628
Water19,6901093
1
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4858
Polymers58,6762
Non-polymers8096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,84514
Polymers58,6762
Non-polymers1,17012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Glutamate receptor 2
F: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,73312
Polymers58,6762
Non-polymers1,05810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.682, 162.582, 47.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glutamate receptor 2 / GRIA2 / 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: 29337.830 Da / Num. of mol.: 6 / Fragment: UNP residues 413-527,UNP residues 653-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLUR2, GRIA2, GLUR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42262

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Non-polymers , 5 types, 1121 molecules

#2: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-9C3 / 9-{4-[(propan-2-yl)oxy]phenyl}-3,4-dihydro-2H-2lambda~6~-pyrido[2,1-c][1,2,4]thiadiazine-2,2-dione


Mass: 318.391 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H18N2O3S
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1093 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 15% PEG 3350, 0.1M SODIUM ACETATE, 0.1M ZINC ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976486 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976486 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 222823 / % possible obs: 95.2 % / Redundancy: 3.4 % / Rsym value: 0.062 / Net I/σ(I): 17.9
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10721 / Rsym value: 0.903 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
cctbx.primedata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTJ

1ftj


Resolution: 1.58→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.911 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.22058 11166 5 %RANDOM
Rwork0.19348 ---
obs0.19484 211606 95.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 31.674 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å20.06 Å2
2--0.06 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.58→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12232 0 166 1093 13491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912836
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.98417280
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55551612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39624.32507
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.113152458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1351566
X-RAY DIFFRACTIONr_chiral_restr0.0890.21893
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5632.2226322
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.383.3257887
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.372.5116514
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.4931.2420020
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 805 -
Rwork0.285 14950 -
obs--91.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83480.0573-0.00730.1432-0.04360.70910.03440.035-0.06820.01090.0182-0.0390.04080.0009-0.05260.02740.0254-0.00230.02590.00140.084432.6637-55.390418.2912
20.3112-0.166-0.0130.3780.00510.5144-0.0309-0.0041-0.001-0.0171-0.0058-0.00020.000800.03670.0079-0.0041-0.00140.04010.00050.010728.42050.028928.2592
30.8070.04110.02130.1640.03350.71070.0340.03430.06570.00780.01470.037-0.0410.0062-0.04870.02510.0232-0.00210.0245-0.0040.076624.166555.456218.2471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A413 - 795
2X-RAY DIFFRACTION1A901 - 902
3X-RAY DIFFRACTION1B413 - 795
4X-RAY DIFFRACTION1B1001
5X-RAY DIFFRACTION2C413 - 795
6X-RAY DIFFRACTION2C1001
7X-RAY DIFFRACTION2D413 - 795
8X-RAY DIFFRACTION2D901
9X-RAY DIFFRACTION3E413 - 795
10X-RAY DIFFRACTION3E1001
11X-RAY DIFFRACTION3F413 - 795
12X-RAY DIFFRACTION3F901

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