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- PDB-4lz8: Crystal structures of GLuR2 ligand-binding-domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 4lz8
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 / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor 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 / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / 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-1YX / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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_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

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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)92,65313
Polymers91,0323
Non-polymers1,62110
Water6,233346
1
A: Glutamate receptor 2
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5397
Polymers60,6882
Non-polymers8525
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-8 kcal/mol
Surface area23060 Å2
MethodPISA
2
B: Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,22712
Polymers60,6882
Non-polymers1,54010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1590 Å2
ΔGint-9 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.676, 164.953, 47.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRMETMETAA394 - 40817 - 31
21THRTHRMETMETBB394 - 40817 - 31
31THRTHRMETMETCC394 - 40817 - 31
12ARGARGALAALAAA420 - 67743 - 177
22ARGARGALAALABB420 - 67743 - 177
32ARGARGALAALACC420 - 67743 - 177
13VALVALCYSCYSAA681 - 773181 - 273
23VALVALCYSCYSBB681 - 773181 - 273
33VALVALCYSCYSCC681 - 773181 - 273
14GLUGLUGLUGLUAD801
24GLUGLUGLUGLUBI804
34GLUGLUGLUGLUCM803

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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-GLU / GLUTAMIC ACID


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


Mass: 426.505 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27FN4O4S
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
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: 49.71 %
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 FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / 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: 1.85→93.659 Å / Num. obs: 74948 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Χ2: 1.633 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.85-1.925.671811.243194.3
1.92-1.996.172871.29195.20.745
1.99-2.086.172201.3721950.469
2.08-2.196.172591.458194.70.298
2.19-2.336.173441.518196.20.217
2.33-2.516.374911.542196.80.158
2.51-2.766.675941.682198.80.103
2.76-3.16776671.845198.60.066
3.16-3.997.177692.053199.40.04
3.99-506.881362.007199.70.03

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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: 1.85→93.659 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2157 / WRfactor Rwork: 0.1844 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8507 / SU B: 6.915 / SU ML: 0.096 / SU R Cruickshank DPI: 0.142 / SU Rfree: 0.1333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 3834 5.1 %RANDOM
Rwork0.1963 ---
obs0.1982 74877 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 100.96 Å2 / Biso mean: 20.2948 Å2 / Biso min: -1.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.85→93.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6035 0 93 346 6474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226263
X-RAY DIFFRACTIONr_bond_other_d0.0020.024348
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9778424
X-RAY DIFFRACTIONr_angle_other_deg1.016310644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01224.39246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15151177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9541530
X-RAY DIFFRACTIONr_chiral_restr0.1150.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021216
X-RAY DIFFRACTIONr_mcbond_it1.0581.53820
X-RAY DIFFRACTIONr_mcbond_other0.3581.51592
X-RAY DIFFRACTIONr_mcangle_it1.81526129
X-RAY DIFFRACTIONr_scbond_it2.92332443
X-RAY DIFFRACTIONr_scangle_it4.4294.52295
Refine LS restraints NCS

Ens-ID: 1 / Number: 3250 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.40.5
2BMEDIUM POSITIONAL0.450.5
3CMEDIUM POSITIONAL0.440.5
1AMEDIUM THERMAL0.82
2BMEDIUM THERMAL0.852
3CMEDIUM THERMAL0.842
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 278 -
Rwork0.431 5002 -
all-5280 -
obs--93.15 %
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)
12.1644-0.57470.37524.3835-0.64912.0762-0.06210.01170.10210.0275-0.05220.1358-0.06720.23270.11430.0357-0.0093-0.00140.08740.01240.018873.08236.58949.18
23.877-0.5748-2.16443.15920.3275.2864-0.4288-0.2263-0.3385-0.15680.0179-0.1670.85050.74140.41090.27210.17340.0780.21890.06790.061180.3221.74132.057
33.07350.43240.05422.2992-0.10142.3182-0.01790.10970.18570.05770.0278-0.05810.08490.2818-0.010.03360.0379-0.01320.0645-0.00480.017570.44375.6258.794
42.30420.0738-0.14914.08090.4942.39740.01260.0695-0.2407-0.0961-0.14510.25250.1361-0.03940.13250.06590.0238-0.00610.0371-0.00910.049660.02362.94841.932
52.62390.0022-0.13724.42110.53562.3348-0.0622-0.0372-0.3024-0.17630.0681-0.270.2214-0.0725-0.00590.0706-0.03230.00520.06490.00080.057749.62117.14248.886
63.2526-0.57341.23552.7061-0.52164.6625-0.13030.08550.2152-0.00880.01180.1781-0.517-0.36360.11850.20220.00180.01660.1446-0.00350.041742.25931.9232.004
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A801
2X-RAY DIFFRACTION1A393 - 499
3X-RAY DIFFRACTION1A732 - 773
4X-RAY DIFFRACTION2A500 - 508
5X-RAY DIFFRACTION2A632 - 728
6X-RAY DIFFRACTION3B804
7X-RAY DIFFRACTION3B394 - 499
8X-RAY DIFFRACTION3B732 - 773
9X-RAY DIFFRACTION4B500 - 508
10X-RAY DIFFRACTION4B632 - 728
11X-RAY DIFFRACTION5C803
12X-RAY DIFFRACTION5C394 - 499
13X-RAY DIFFRACTION5C732 - 773
14X-RAY DIFFRACTION6C500 - 508
15X-RAY DIFFRACTION6C632 - 728

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