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- PDB-5zg3: Crystal structure of the GluA2o LBD in complex with glutamate and... -

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Basic information

Entry
Database: PDB / ID: 5zg3
TitleCrystal structure of the GluA2o LBD in complex with glutamate and TAK-137
ComponentsGlutamate receptor 2
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-9C6 / ACETATE ION / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)179,40138
Polymers176,0276
Non-polymers3,37432
Water19,1321062
1
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5719
Polymers58,6762
Non-polymers8967
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)60,01016
Polymers58,6762
Non-polymers1,33414
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)59,82013
Polymers58,6762
Non-polymers1,14411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.065, 162.332, 47.385
Angle α, β, γ (deg.)90.00, 90.02, 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 / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P42262

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Non-polymers , 5 types, 1094 molecules

#2: Chemical ChemComp-9C6 / 9-(4-phenoxyphenyl)-3,4-dihydro-2H-2lambda~6~-pyrido[2,1-c][1,2,4]thiadiazine-2,2-dione


Mass: 352.407 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H16N2O3S
#3: Chemical
ChemComp-GLU / GLUTAMIC ACID


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


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1062 / 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: 50.65 %
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 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976486 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 205163 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rsym value: 0.062 / Net I/σ(I): 19
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10200 / Rsym value: 0.841 / % possible all: 99.1

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Processing

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

1ftj


Resolution: 1.65→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.205 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.21486 10299 5 %RANDOM
Rwork0.18417 ---
obs0.18571 194547 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 31.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å20.13 Å2
2--0.08 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12232 0 191 1062 13485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212735
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9817112
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4651584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21224.308506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.702152427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.671566
X-RAY DIFFRACTIONr_chiral_restr0.0960.21881
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029208
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_it2.0392.5586298
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9324.2937845
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3523.1066437
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.86127.96519721
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: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 714 -
Rwork0.278 14054 -
obs--96.59 %
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)
10.88360.044-0.00630.1973-0.02330.64640.03650.0498-0.06360.00060.0039-0.04720.026-0.0165-0.04040.04910.0148-0.0150.0241-0.00190.102932.6989-55.40918.1998
20.4079-0.2029-0.00180.43830.00140.4762-0.02770.00110.0005-0.022-0.0016-0.0008-0.0039-0.00120.02930.0335-0.0097-0.00620.03810.00080.012328.4940.044528.2865
30.85930.03640.01170.18540.02540.63880.03670.04420.0697-0.00210.01220.0476-0.02070.0193-0.04890.06070.01640.00380.0334-0.00120.148224.325255.479418.2568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A413 - 795
2X-RAY DIFFRACTION1A1002
3X-RAY DIFFRACTION1B413 - 795
4X-RAY DIFFRACTION1B901
5X-RAY DIFFRACTION1A1001
6X-RAY DIFFRACTION2C413 - 795
7X-RAY DIFFRACTION2C901
8X-RAY DIFFRACTION2D413 - 795
9X-RAY DIFFRACTION2D901
10X-RAY DIFFRACTION2C1001
11X-RAY DIFFRACTION3E413 - 795
12X-RAY DIFFRACTION3E1002
13X-RAY DIFFRACTION3F413 - 795
14X-RAY DIFFRACTION3F901
15X-RAY DIFFRACTION3E1001

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